Abstract 4820: Selective CDK7 inhibitors suppress super enhancer-genes, induce massive apoptosis in acute myeloid leukemia and demonstrate durable in vivo efficacy
Authors: Hu Shanhu , Ke Nan , Ren Yixuan , Lopez Jeremy , Miljovska Sofija , Orlando David , Schmidt Darby , Bradley Michael , Sprott Kevin , Olson Eric , Fritz Christian C. , Choi Yoon Jong 
Published: July 2016

Abstract
CDK7 acts bi-functionally as a CDK-activating kinase (CAK) controlling proliferation and as a transcriptional kinase phosphorylating the CTD-RNA Pol II, driving efficient transcriptional processes. CDK7 has recently emerged as an attractive gene control target in cancers addicted to oncogenic transcription factors, regulated by super-enhancers (SEs), (Kwiatkowski et al., 2014; Chipumuro et al., 2014; Christensen 2014; Wang 2015). Acute Myeloid Leukemias (AML) harbor a heterogeneous set of mutations resulting in an altered cell state and aberrant epigenetic and transcriptional control, yet lack targeted therapeutic options. Employing our SE-platform technology we reveal mechanistic insights underlying the vulnerability of AML to gene control modulation via selective CDK7 inhibition.
We describe first-in-class CDK7 inhibitors that covalently target a cysteine outside the kinase domain, resulting in sustained, highly selective inhibition. Several lead compounds exhibit significant biochemical potency (Ki = 10-60 nM and kinact = 5-13/h) and exquisite selectivity when profiled against &gt;400 other kinases. In a cancer cell line panel, acute leukemias emerged among the most sensitive to CDK7 inhibition. Moreover, AML cell lines undergo rapid and robust apoptosis within 24 hours. This is preceded by CDK7 target engagement and concomitant loss of P-CTD-RNAPolII suggesting the primary consequence of CDK7 inhibition is the impaired transcriptional activity of CDK7. Further investigation of the transcriptional consequences of CDK7 inhibition point to a reliance on key disease relevant SE-genes (e.g. MYB, HOX10A and MYC) that are predominantly reduced.
Given the covalent mechanism of our CDK7 inhibitors and PK profile in vivo, we use short treatments in vitro with subsequent washout of free drug to model intermittent dosing regimens in vivo. We demonstrate that short drug exposures maintain a robust irreversible apoptotic response in leukemia cells. In contrast, treated non-transformed cells recover from a transient G2/M arrest followed by re-synthesis of free CDK7 and no apoptosis/cell death. We have extended these findings to in vivo experiments whereby intermittent dosing in AML patient derived xenograft models (PDX) maintains efficacy (reducing human CD45+ leukemia cells to &lt;1%) and significant survival advantage. We have established a PD assay by measuring target engagement of CDK7 both in mouse xenografts and human blood to support: 1) establishing a PK-PD-efficacy relationship 2) quantifying target engagement during dose escalation in a Ph1 clinical trial.
In summary, we describe first-in-class CDK7 inhibitors that are potent and selective and lead to durable, complete responses in PDX models of AML. These data support the rationale for advancing one or more members of this class of compounds toward clinical development.
Citation Format: Shanhu Hu, Nan Ke, Yixuan Ren, Jeremy Lopez, Sofija Miljovska, David Orlando, Darby Schmidt, Michael Bradley, Kevin Sprott, Eric Olson, Christian C. Fritz, Yoon Jong Choi. Selective CDK7 inhibitors suppress super enhancer-genes, induce massive apoptosis in acute myeloid leukemia and demonstrate durable in vivo efficacy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4820.