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Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (ATAC-seq)

ABSTRACT: Silencing of the somatic cell-type specific gene expression programs is a critical yet poorly understood step in nuclear reprogramming. To uncover chromatin-related pathways important for maintaining cell identity, we carried out a reprogramming screen using inhibitors of chromatin factors. Here we identify two independent acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators EP300 and CBP as potent enhancers of reprogramming. EP300/CBP bromodomain inhibition is critical during early stages of reprogramming, significantly accelerates the emergence of iPSCs and, when combined with Dot1L inhibition, enables efficient derivation of human iPSCs with Oct4 and Sox2 alone. In contrast, complete inhibition of catalytic acetyl-transferase activity of EP300/CBP prevents reprogramming. Genome-wide expression analyses indicate that EP300/CBP bromodomain inhibition diminishes the expression of somatic-specific genes without affecting the induction of pluripotency regulators. Through expression analyses, we identify the master mesenchymal transcription factor PRRX1 as a functionally important target in reprogramming that is downregulated upon EP300/CBP bromodomain inhibition. Collectively, our data uncover a role for bromodomain-mediated interactions of EP300/CBP in sustaining cell type specific gene expression programs and maintaining somatic cell identity

ORGANISM(S): Homo sapiens

PROVIDER: GSE118218 | GEO | 2019/02/14

REPOSITORIES: GEO

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Project description:EP300 and CBP are paralogous, multidomain histone acetyltransferases (HATs) that regulate gene expression by binding to and acetylating diverse proteins. With widespread effects on gene regulation, these enzymes are attractive targets for therapeutic development. Discovery efforts for chemical inhibitors typically target protein domains that are amenable to probe binding. In some cases, probes have been identified for more than one domain within a single protein, including high potency inhibitors of both the catalytic HAT domain and bromodomain (BRD) that mediate the enzymatic and protein binding (“reader”) activities of EP300/CBP. In cancer cell systems, combination inhibition of both domains is more toxic than single inhibitor alone, indicating that inhibition of individual domain functions may elicit differential effects. Thus, we hypothesized that determining the relative effects of domain-specific inhibition of EP300/CBP on tumor cell growth may elucidate exceptional-responding tumor types to one inhibitor or the other. This would permit a broader therapeutic index by enabling reduced dosing of domain-targeted inhibitors, while maintaining enhanced inhibition of cancer cell growth. Here, using high-throughput cell line-based screening, we demonstrate that targeting the HAT or BRD domains of EP300/CBP using the chemical probes A485 and CCS1477 has differential effects in select tumor types. Group 3 medulloblastoma (G3MB) cells were especially sensitive to EP300/CBP BRD inhibition, as compared with HAT inhibition. Structurally, these effects are mediated by the difluorophenyl group in the catalytic core of CCS1477. Mechanistically, the effects of bromodomain and HAT-domain specific inhibition are distinct, with bromodomain inhibition causing rapid early disruption of genetic dependency networks that are required for G3MB growth. These studies provide a domain-specific structural foundation for drug discovery efforts targeting EP300/CBP and identify a selective role for the EP300/CBP bromodomain in maintaining genetic dependency networks in G3MB cells.

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Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (ATAC-seq)

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