Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment

NUT carcinoma (NC), characterized most commonly by the BRD4-NUTM1 fusion, is a rare, aggressive variant of squamous carcinoma with no effective treatment. BRD4-NUT drives growth and maintains the poorly differentiated state of NC by activating pro-growth genes such as MYC, through the formation of massive, hyperacetylated, superenhancer-like domains termed megadomains. BRD4-NUT-mediated hyperacetylation of chromatin is facilitated by the chromatin-targeting tandem bromodomains of BRD4, combined with NUT, which recruits the histone acetyltransferase, p300. Here, we developed a high-throughput small-molecule screen to identify inhibitors of transcriptional activation by NUT. In this dCAS9-based GFP-reporter assay, the strongest hits were diverse histone deacetylase (HDAC) inhibitors. Two structurally unrelated HDAC inhibitors, panobinostat and the novel compound, IRBM6, both repressed growth and induced differentiation of NC cells in proportion to their inhibition of NUT transcriptional activity. These two compounds repressed transcription of megadomain-associated oncogenic genes, such as MYC and SOX2, while upregulating pro-differentiation, non-megadomain-associated genes, including JUN, FOS, and key cell-cycle regulators, such as CDKN1A. The transcriptional changes correlate with depletion of BRD4-NUT from megadomains, and redistribution of the p300/CBP-associated chromatin acetylation mark, H3K27ac, away from megadomains toward regular enhancer regions previously populated by H3K27ac. In NC xenograft models, we demonstrated that suppression of tumor growth by panobinostat was comparable with that of bromodomain inhibition, and when combined they improved both survival and growth suppression. IMPLICATIONS: The findings provide mechanistic and preclinical rationale for the use of HDAC inhibitors, alone or combined with other agents, in the treatment of NUT carcinoma.

Combined Targeting of the BRD4-NUT-p300 Axis in NUT Midline Carcinoma by Dual Selective Bromodomain Inhibitor, NEO2734

NUT midline carcinoma (NMC) is a rare, aggressive subtype of squamous carcinoma that is driven by the BRD4-NUT fusion oncoprotein. BRD4, a BET protein, binds to chromatin through its two bromodomains, and NUT recruits the p300 histone acetyltransferse (HAT) to activate transcription of oncogenic target genes. BET-selective bromodomain inhibitors have demonstrated on-target activity in patients with NMC, but with limited efficacy. P300, like BRD4, contains a bromodomain. We show that combining selective p300/CBP and BET bromodomain inhibitors, GNE-781 and OTX015, respectively, induces cooperative depletion of MYC and synergistic inhibition of NMC growth. Treatment of NMC cells with the novel dual p300/CBP and BET bromodomain-selective inhibitor, NEO2734, potently inhibits growth and induces differentiation of NMC cells in vitro; findings that correspond with potentiated transcriptional effects from combined BET and p300 bromodomain inhibition. In three disseminated NMC xenograft models, NEO2734 provided greater growth inhibition, with tumor regression and significant survival benefit seen in two of three models, compared with a lead clinical BET inhibitor or "standard" chemotherapy. Our findings provide a strong rationale for clinical study of NEO2734 in patients with NMC. Moreover, the synergistic inhibition of NMC growth by CBP/p300 and BET bromodomain inhibition lays the groundwork for greater mechanistic understanding of the interplay between p300 and BRD4-NUT that drives this cancer.

Abstract B014: Novel dual BET/p300 bromodomain inhibitors therapeutically inhibit BRD4-NUT driven NUT Carcinomas

Introduction: NUT carcinoma (NC) is an aggressive subtype of squamous carcinoma whose growth is driven by the BRD4-NUT fusion oncoprotein. With a median survival of 6.7 months, NC is perhaps the most aggressive solid tumor in humans, and there exist no effective or standard treatment regimens. BRD4-NUT drives growth by blocking differentiation. BRD4-NUT binds chromatin through the acetyl-histone binding, dual bromodomains (BD) of BRD4. BET inhibitors are highly selective for the BDs of BET proteins and have demonstrated on-target activity in human NC patients, however toxicity has limited efficacy. BRD4-NUT forms hyperacetylated regions, termed megadomains, enriched with the NUT-interacting histone acetyltransferase, p300, that upregulate expression of key oncogenic targets, including MYC. Here we sought to determine the role of p300 in the blockade of differentiation and growth of NC cells. Next, we investigated whether inhibiting both BRD4 and p300, by blocking the BDs of BRD4 and p300 with a novel dual inhibitor class of compounds, termed ‘NEO’ (NEO2734 and NEO1132), might exhibit greater inhibition of NC growth than BET BD inhibition alone. Methods: We utilized in vitro reporter assays to map the minimal essential domain of NUT necessary for its interaction with p300. Using our NC cell derivative, 797TRex, which contains a single genomic FRT recombination site, and constitutively express tetracycline repressor (TR), allows for FLP-recombinase insertion of tet-inducible NUT or p300 constructs. Immunofluorescence, immunoblotting, cell-titer glo (Promega), and nascent RNAseq were used to evaluate effects of transgene induction and treatment with compounds. Tolerability and efficacy of various compounds were evaluated in vivo in a disseminated mouse NC xenograft model using the PER-403 human BRD4-NUT+ cell line. Results: We determined that a putative transcriptional activation domain (TAD1 (NUT390-482)) of NUT and the TAZ2 domain of p300 (p3001721-1837) bind directly. We found that inducing expression of TAD1 or TAZ2 in 797TRex cells results in rapid differentiation and promotes the dispersion of acetylated and p300-enriched BRD4-NUT megadomains/foci, indicating that p300 is required for the blockade of differentiation through its direct interaction with NUT. Preliminary data also suggest TAD1 (NUT390-482) expression in 797TRex cells decreases nascent transcription of BRD4-NUT-mediated oncogenic targets. Furthermore, our findings indicate that NEO compounds inhibit in vitro NC growth with IC50s = 44-225nM, which associated with the induction of squamous differentiation. Most strikingly, the lead clinical NEO compound completely abrogated NC tumor growth in our pilot disseminated xenograft mouse study, which greatly prolonged survival as compared to a lead clinical BET inhibitor (GSK762) or “standard” chemotherapy (cisplatin/etoposide) commonly used for NC. Conclusions: These data support our hypothesis that p300 recruitment is necessary for the oncogenic functions of BRD4-NUT and dual targeting of BET and p300 BDs represents a promising therapeutic option for NC patients. Future studies are necessary to determine the relative contribution of BET versus p300 BD inhibition to preventing NC growth by NEO compounds.

Citation Format: Chevaun D Morrison-Smith, Amy DiBona, Erica Walsh, Kristina Danga, Ivona Filic, Tatiana Knox, Adlai Grayson, Michael Cameron, Christopher French. Novel dual BET/p300 bromodomain inhibitors therapeutically inhibit BRD4-NUT driven NUT Carcinomas [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B014. doi:10.1158/1535-7163.TARG-19-B014