Targeting the Transcriptional Addiction of Leukemia Stem Cells by a New Class of Protein Kinase Inhibitors

CKIα ablation is a promising means of activating p53 and killing leukemia cells in MDS and AML. Yet we found that CKIα ablation or degradation which activates p53 was not sufficient to selectively eliminate leukemia stem cells, due to robust expression of anti-apoptotic oncogenes driven by super-enhancer (SE) activation. We succeeded in developing CKIα inhibitors, targeting the catalytic pocket of CKIα and a special class which co-target CDK9 and suppress the RNA Pol II elongation factor P-TEFb (CDK9-CyclinT1 complex). We found that CKIα inhibitors possessing potent anti-leukemia activity are distinguished by their capacity to inhibit P-TEFb, evident by blocking the phosphorylation of RNA Pol II C-terminal domain (pCTD2/5), which controls the rate limiting step transcription and functions as a gatekeeper of SEs. The efficient P-TEFb-targeting activity of the inhibitors enables a selective blockade of leukemia SE-driven transcription. As a result, SE-dependent transcription of major leukemia drivers including Myc and the anti-apoptotic oncogenes Bcl-2 and Mcl-1 was nearly abolished. Rapid p53 induction with disruption of oncogenic super-enhancers eliminates leukemia stem cells without compromising normal HSPCs.