Synergistic Anti-Tumor Effect of Combining Selective CDK7 and BRD4 Inhibition in Neuroblastoma

Abstract

PurposeCyclin-dependent kinases (CDKs) that have critical roles in RNA polymerase II (Pol II)-mediated gene transcription are emerging as therapeutic targets in cancer. We have previously shown that THZ1, a covalent inhibitor of CDKs 7/12/13, leads to cytotoxicity in MYCN-amplified neuroblastoma through the downregulation of super-enhancer-associated transcriptional upregulation. Here we determined the effects of YKL-5-124, a novel covalent inhibitor with greater selectivity for CDK7 in neuroblastoma cells.Experimental DesignWe tested YKL-5-124 in MYCN-amplified and nonamplified neuroblastoma cells individually and in combination with other inhibitors in cell line and animal models. Cell viability, target validation, effects on cell cycle and transcription were analyzed.ResultsCDK7 inhibition with YKL-5-124 did not lead to significant cell death, but resulted in aberrant cell cycle progression especially in MYCN-amplified cells. Unlike THZ1, YKL-5-124 had minimal effects on Pol II C-terminal domain phosphorylation, but significantly inhibited that of the CDK1 and CDK2 cell cycle kinases. Combining YKL-5-124 with the BRD4 inhibitor JQ1 resulted in synergistic cytotoxicity. A distinct MYCN-gene expression signature associated with resistance to BRD4 inhibition was suppressed with the combination. The synergy between YKL-5-124 and JQ1 translated into significant tumor regression in cell line and patient-derived xenograft mouse models of neuroblastoma.ConclusionsThe combination of CDK7 and BRD4 inhibition provides a therapeutic option for neuroblastoma and suggests that the addition of YKL-5-124 could improve the therapeutic efficacy of JQ1 and delay resistance to BRD4 inhibition.

The BRD4 Inhibitor dBET57 Exerts Anticancer Effects by Targeting Superenhancer-Related Genes in Neuroblastoma

“…PROTACs are heterobifunctional molecules that can ubiquitinate and degrade target proteins by recruiting E3 ligases to target proteins. It precisely targets BRD4 proteins, induces the degradation of BRD2 and BRD3, and has a strong antitumor effect on neuroblastoma [20]. In order to evaluate the anti-NB effect of dBET57, NB cells and 4 normal cells were treated in a concentration gradient for 72 hours.…”

“…More specifically, BRD4 inhibitors targeting ubiquitin-mediated hydrolysis of MYCN to treat NB have important significance and application prospects. In recent years, clinical trials of BRD4 inhibitors have shown that early acquired resistance limits their therapeutic benefits [20]. In this study, we investigated dBET57, a heterobifunctional molecule inhibitor that binds the target protein at one end and the E3 ubiquitin ligase (CRBN binding fragment) at the other end.…”

BET Bromodomain Degradation Disrupts Function but Not 3D Formation of RNA Pol2 Clusters

“…The increase in the RNA Pol2 loading ratio, but not the pausing ratio, suggests a separate mechanism from CDK9. CDK7 phosphorylates serine 5 of Pol2 at the promoter to promote initiation [ 32 ], and it has been shown that CDK7 inhibitors have a synergistic effect when combined with BRD4 inhibitors in neuroblastoma [ 33 ], so a local increase in CDK7 could also be implicated. Another possibility is that BRD4 at super enhancers is involved in the unloading of Pol2 during termination.…”

Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status

“…THZ2 has improved pharmacokinetic features compared with THZ1, with a 5-fold improved half-life in vivo [ 238 ]. Some other CDK7 inhibitors, for example, SY-1365 and YKL-5-124, show covalent binding to CDK7 and also have low IC50 and positive effects in ovarian and breast cancer, and neuroblastoma, respectively [ 240 , 241 ] ( Table 3 ). SY-1365 clinical studies are terminated due to business decisions (NCT03134638).…”