Abstract 2980: Therapeutic potential of combined targeting of casein kinase 1 alpha (CK1 alpha) and CDK7/9 with the inhibitor BTX-A51 in human liposarcomas

Abstract Introduction: Liposarcomas (LPS) are mesenchymal cell malignancies that are diagnosed in more than 3500 patients in the US each year. LPS are characterized by DNA amplifications of MDM2 (100%) and CDK4 (90+%) genes on neochromosomes, generally with wild-type TP53. Management of metastatic or surgically unresectable LPS remains purely palliative. Recent clinical trials targeting MDM2 or CDK4/6 with small-molecule inhibitors have shown modest activity but have generally failed in phase 3 trials. The development of new therapeutics is greatly needed to improve outcomes for patients with LPS. Results: To identify unique liposarcoma-specific vulnerabilities, we utilized the Dependency Map (DepMap) database to analyze gene-specific dependencies of 9 LPS cell lines as compared to non-LPS cancers and identified CSNK1A1 as one of the top essential genes preferentially for LPS. siRNA-mediated depletion of CSNK1A1 confirmed that CK1α negatively regulates p53 and is critical for the proliferation and survival of LPS cells. DepMap analyses identified CDK7 and CDK9 as two additional top LPS-essential genes. Three CDK9 inhibitors suppressed LPS cell growth and induced apoptosis by decreasing MDM2 levels while inducing expression of p53 and PUMA. The cytotoxic effects of CDK9 inhibitors were enhanced upon CK1α depletion. Furthermore, we quantitatively determined synergism between CDK7 and CDK9 inhibitors in LPS cells. These data led us to examine combined targeting of CK1α and CDK7/9 in LPS with the novel small molecule inhibitor BTX-A51, which has previously also been shown to inhibit CK1α, CDK7, and CDK9 with nanomolar potency in acute myeloid leukemia (AML) models. BTX-A51 treatment significantly reduced expression of MDM2 with marked induction of p53, resulting in increased PUMA expression and profound apoptosis of LPS cells. Through CRISPR/Cas9-mediated TP53 knockout, we established that BTX-A51-treatment-induced apoptosis was in part mediated in a p53-dependent manner, which was further validated transcriptionally using RNA-Seq based pathway analysis. BTX-A51 also reduced expression of the apoptosis inhibitor MCL1 and primed LPS cell lines and PDX-derived cells for BIM/PUMA-induced apoptosis. Importantly, in vivo experiments in two LPS PDX models demonstrated that BTX-A51 is well-tolerated with anti-tumor efficacy. Conclusions: These data have confirmed CK1α, CDK9, and CDK7 as essential for LPS cells and indicate that BTX-A51 has potent preclinical efficacy in LPS, through combined inhibition of CK1α, CDK9, and CDK7. Our data form the scientific foundation for our ongoing pilot clinical trial evaluating BTX-A51 in patients with advanced WDLPS or DDLPS (NCT06414434). Citation Format: Renyan Liu, Nicole L. Solimini, Caoibhne McSweeney, Patrick Bhola, Daryl Griffin, Tim B. Branigan, Michael J. Wagner, Audrey Turchick, Ricardo de Simoes, Joshua M. Dempster, Jie Hao, Xin Wang, Roshen Alharthi, Michael Yorsz, Shaili Soni, Cing-siang Hu, Irit Snir-Alkalay, Francisca Vazquez, Prafulla C. Gokhale, Constantine Mitsiades, Anthony Letai, Yinon Ben-Neriah, George D. Demetri, Geoffrey I. Shapiro. Therapeutic potential of combined targeting of casein kinase 1 alpha (CK1 alpha) and CDK7/9 with the inhibitor BTX-A51 in human liposarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2980.