Targeted Degradation of CDK9 Potently Disrupts MYC Network

Cyclin-dependent kinase 9 (CDK9) coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release states. It is an important co-factor for transcription factors, such as MYC, that drive aberrant cell proliferation when their expression is deregulated. CDK9 modulation offers an approach for attenuating dysregulation in such transcriptional programs. As a result, numerous drug development campaigns to inhibit CDK9 kinase activity have been pursued. We validated that CDK9 inhibition triggers a compensatory mechanism that dampens its effect on MYC transcriptional programs and found that this resistance mechanism was absent when the Kinase is degraded. Importantly, CDK9 degradation is more effective than its inhibition for disrupting MYC transcriptional regulatory circuitry likely through the abrogation of both enzymatic and scaffolding functions of CDK9. Three or four replicates each of 3 cell lines (MOLT4, PSN1 or RH1) treated with either DMSO (vehicle control), KB-0742 (CDK9 inhibitor) or KI-CDK9d-32 (CDK9 degrader) for 2hr, 4hr or 8hr.