CDK9 recruits HUWE1 E3 ligase to degrade RARα in a kinase independent manner and offers therapeutic opportunities for cutaneous T-cell lymphoma

Abstract Cutaneous T-cell lymphoma (CTCL) is a highly heterogeneous non-Hodgkin lymphoma that originates from the skin and invades the systemic hematopoietic system. Current skin-directed or systemic treatment including chemotherapy, retinoid analogs, interferons, HDAC inhibitors and monoclonal antibodies yielded limited clinical responses with high incidence of side effects, emphasizing urgent clinical need for more effective targeted therapy. Here, through small inhibitors library screening, we identify cyclin dependent kinase 9 (CDK9) as a driver for growth of CTCL. Single-cell RNA-seq data analyses reveal a CDK9high malignant T cell cluster with a unique actively proliferating feature. Pharmacological inhibition, genetic depletion or proteolysis targeting chimera (PROTAC)-medicated degradation of CDK9 significantly inhibit the growth of CTCL cells in vitro and in preclinical murine models. Beyond established kinase-dependent modulation on RNA polymerase II activity, CDK9 protein promotes degradation of retinoid acid receptor α (RARα) at lysine 360 in a kinase-independent manner via recruiting the HECT domain containing E3 ligase HUWE1. Depletion of CDK9 protein thus accumulates RARα and enhances the sensitivity of CTCL cells to all-trans retinoid acid (ATRA) which induces growth arrest and T cell differentiation. Co-administration of CDK9-PROTAC (GT-02897) with ATRA leads to synergistic attenuation of tumor growth in vitro and in xenograft models, providing a potential translational treatment for complete eradication of CTCL.