Abstract 1959: CDK9 inhibition combined with hypomethylating agents target MCL-1 dependency in MDS and AML
Authors: Matsumura Yuta , Tyagi Ethika , Pathi Satya , Vo Dan D. , Zhu Tianxiang , Verma Suman , Whatcott Clifford J. , Anthony Stephen P. , Siddiqui Adam , Foulks Jason M. , Bearss David J. , Warner Steven L. 
Published: July 2021

Abstract
Myelodysplastic syndrome (MDS) is a heterogeneous group of hematopoietic stem cell disorders. Approximately 70% of patients diagnosed with higher-risk (HR) MDS progress to acute myeloid leukemia (AML). Cyclin-dependent kinase 9 (CDK9) influences transcription through phosphorylation and activation of RNA polymerase II (RPB1), which increases the levels of key oncogenic survival genes like myeloid cell leukemia-1 (MCL-1). MCL-1 dependent malignancies can be identified through a functional assay by adding a NOXA mimetic MCL-1 antagonist peptide to patient samples and measuring the subsequent induction of apoptosis. The assay has been tested in bone marrow mononuclear cells (BMMCs) from AML and MDS patients to examine MCL-1 dependency prior to therapy with alvocidib. Approximately 25% of AML patient BMMCs and 60% of MDS patient BMMCs are MCL-1 dependent (data not shown). We hypothesized that the hypomethylating agents (HMAs) azacitidine and decitabine, which are currently approved for treatment of MDS, can increase MCL-1 dependency through re-expression of pro-apoptotic proteins like NOXA, normally repressed through DNA methylation in malignancies. In the MV-4-11 AML cell line and primary CD34+ MDS BMMCs, alvocidib treatment resulted in a dose dependent reduction in p-RPB1 and MCL-1. In cell viability assays using CellTiter-Glo, treatment with alvocidib and azacitidine resulted in IC50 values of ~100 nM and ~3000 nM, respectively in both cell types. Treatment with HMAs increased NOXA expression and alvocidib suppressed MCL-1 expression, whereas sequential treatment of azacitidine and alvocidib showed both NOXA induction and MCL-1 suppression. Sequential treatment of azacitidine and alvocidib showed synergistic apoptosis induction compared with either treatment alone. Azacitidine treatment sensitized MV-4-11 and MDS BMMCs to MCL-1 inhibition in an MCL-1 dependency assay. In an in vivo efficacy study using the MOLM13 AML xenograft model, the combination of alvocidib and azacitidine or decitabine inhibited tumor growth 71% and 84%, respectively. Alvocidib, azacitidine and decitabine alone showed 51%, 5.7% and 19% tumor growth inhibition (TGI), respectively. Pharmacodynamic analysis in a Phase 1 trial with alvocidib (clinicaltrials.gov, NCT03593915) showed DNA methylation of NOXA gene locus was reduced and NOXA gene expression was upregulated, while MCL-1 gene expression was suppressed in peripheral blood mononuclear cells (PBMCs) after azacitidine and alvocidib treatment. These pre-clinical and clinical data suggest that an alvocidib/HMA combination may constitute a viable therapeutic regimen whose rationale focuses on hypertargeting of NOXA/MCL-1. Taken together, these studies indicate that the combination of alvocidib and HMAs drives AML/MDS cells toward MCL-1 dependent apoptosis.
Citation Format: Yuta Matsumura, Ethika Tyagi, Satya Pathi, Dan D. Vo, Tianxiang Zhu, Suman Verma, Clifford J. Whatcott, Stephen P. Anthony, Adam Siddiqui, Jason M. Foulks, David J. Bearss, Steven L. Warner. CDK9 inhibition combined with hypomethylating agents target MCL-1 dependency in MDS and AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1959.