Mechanistic understanding of a novel CBP/p300 inhibitor in fusion-positive rhabdomyosarcoma

Fusion-positive rhabdomyosarcoma (FP-RMS) is a pediatric soft tissue carcinoma characterized by poor survival rate and limited therapeutic options. The fusion oncoprotein PAX3-FOXO1 (P3F) is the key driver for FP-RMS, and its transcriptional activity is dependent on histone acetyltransferase CBP/p300. Given the challenge of directly targeting the transcription factor P3F, CBP/p300 represents an attractive therapeutic target in treating FP-RMS. Through a focused screening of different epigenetic-modifying agents against FP-RMS, the inhibition of CBP/p300 emerged as the most effective strategy in selectively suppressing P3F-driven transcriptional activity. To overcome the limitations, such as toxicity and efficacy of the existing CBP/p300 inhibitors, we employed structure-based drug design to develop a potent CBP/p300 dual inhibitor, IHK-44. We used chemical genetic approaches to enable precise and temporal control of its function in investigating the underlying mechanism of CBP/p300 in the context of FP-RMS. In studying the basis of IHK-44's selectivity and potency in FP-RMS compared to other CBP/p300 inhibitors and degraders, we conducted a comprehensive series of studies, including luciferase reporter assays, live-cell imaging, RNA-seq, ChIP-seq, and proteomics. These studies revealed that FP-RMS exhibits unique epigenetic dependencies, particularly at 3D clusters of histone acetylation lacking CpG islands. The predictor of gene responsiveness to CBP/p300 inhibition with IHK-44 is to be found by mapping the 3D enhancer/promoter loops into clusters and quantifying the extent of CpG island involvement in the elements that make up clusters. Genes driven CpG-poor clusters, often very rich in enhancers, are hypersensitive to IHK-44, while CpG-rich clusters, usually promoter-rich, are recalcitrant. This allows us to define clear categorization to distinct types of gene regulation hubs in the cancer epigenome. High-throughput screening across 900 cell lines revealed that FP-RMS is one of the cancer subtypes most sensitive to IHK-44, whereas normal cell lines and fusion-negative RMS were resistant. In summary, our findings suggest a novel therapeutic strategy for FP-RMS by targeting CBP/p300 and highlight the potential of IHK-44 as a promising candidate for further preclinical development.