Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma
Evon Poon, … , Charles Y. Lin, Louis Chesler
Evon Poon, … , Charles Y. Lin, Louis Chesler
Published October 5, 2020
Citation Information: J Clin Invest. 2020;130(11):5875-5892. https://doi.org/10.1172/JCI134132.
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Research Article Oncology

Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma

Abstract

The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuroblastoma, a pediatric cancer in which MYCN amplification is strongly associated with unfavorable outcome. Here, we show that CYC065 (fadraciclib), a clinical inhibitor of CDK9 and CDK2, selectively targeted MYCN-amplified neuroblastoma via multiple mechanisms. CDK9 — a component of the transcription elongation complex P-TEFb — bound to the MYCN-amplicon superenhancer, and its inhibition resulted in selective loss of nascent MYCN transcription. MYCN loss led to growth arrest, sensitizing cells for apoptosis following CDK2 inhibition. In MYCN-amplified neuroblastoma, MYCN invaded active enhancers, driving a transcriptionally encoded adrenergic gene expression program that was selectively reversed by CYC065. MYCN overexpression in mesenchymal neuroblastoma was sufficient to induce adrenergic identity and sensitize cells to CYC065. CYC065, used together with temozolomide, a reference therapy for relapsed neuroblastoma, caused long-term suppression of neuroblastoma growth in vivo, highlighting the clinical potential of CDK9/2 inhibition in the treatment of MYCN-amplified neuroblastoma.

Authors

Evon Poon, Tong Liang, Yann Jamin, Susanne Walz, Colin Kwok, Anne Hakkert, Karen Barker, Zuzanna Urban, Khin Thway, Rhamy Zeid, Albert Hallsworth, Gary Box, Marli E. Ebus, Marco P. Licciardello, Yordan Sbirkov, Glori Lazaro, Elizabeth Calton, Barbara M. Costa, Melanie Valenti, Alexis De Haven Brandon, Hannah Webber, Nicolas Tardif, Gilberto S. Almeida, Rossitza Christova, Gunther Boysen, Mark W. Richards, Giuseppe Barone, Anthony Ford, Richard Bayliss, Paul A. Clarke, Johann De Bono, Nathanael S. Gray, Julian Blagg, Simon P. Robinson, Suzanne A. Eccles, Daniella Zheleva, James E. Bradner, Jan Molenaar, Igor Vivanco, Martin Eilers, Paul Workman, Charles Y. Lin, Louis Chesler

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Figure 4

Pharmacologic blockade of CDK9 targets MYCN-dependent transcriptional landscape.

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Pharmacologic blockade of CDK9 targets MYCN-dependent transcriptional la...
(A) Gene tracks of chromatin accessibility (shown by ATAC-Seq, green), active chromatin marker: H3K27ac (blue) and CDK9 (black) occupancy at MYCN amplicon in Kelly cells. (B) Heatmaps of H3K27ac (blue), MYCN (red), and CDK9 (black) occupancy at all promoters (left) or enhancers (right) ranked by H3K27ac signal. Each row of heatmaps suggests 1 promoter region or enhancer region. The middle of heatmaps indicates the TSS or enhancer centers. (C–E) Left: gene tracks of H3K27ac (blue), MYCN (red), and CDK9 (black) (±CYC065) occupancy at individual loci. ChIP-Seq occupancy is provided in units of rpm/bp. Canonical MYCN-binding sites (red lines) and noncanonical MYCN-binding sites (black lines) are indicated below gene tracks. Right: bar plots of corresponding gene expression normalized to control showing effect of CYC065 (1 μM; 1 hour) treatment. Data are represented as mean ± SD. Two-tailed Student’s t test. *P < 0.05; **P < 0.01. (F) Scatter plot of log2 gene expression (FPKM) fold changes (CYC065; 1 μM; 1 hour) treatment vs. DMSO control (x axis) versus significance of the change (y axis, –log10 FDR value). Genes with 1.5-fold or greater change in expression at an FDR of 0.1 or less are considered differentially expressed (blue and red). (G) The top 5000 transcriptionally active, expressed, and MYCN-associated genes are ranked by MYCN load (promoter + enhancer MYCN). Box plot implicating the log2 mRNA fold change of the top 1000 genes and the log2 mRNA fold change of the other 4000 genes. Two-tailed Student’s t test. (H) Heatmap indicating the mRNA log2 FPKM fold change from the FPKM median of TFs in adrenergic (Adren) and mesenchymal (Mes) core regulatory circuitries, with CYC065 (1 μM; 1 hour) treatment in Kelly cells.