Linking CDK6 to extracellular vesicles – CDK6

Wider research context:
Intracellular and extracellular vesicles (IVs and EVs) are highly heterogeneous organelles with fundamental roles in cellular homeostasis and malignant transformation. Deregulation of vesicle biogenesis and release is described to be a feature of transformation and disease progression by remodeling the malignant niche. Interfering with vesicle biogenesis is a developing new therapeutic direction.

Research question:
Cyclin-dependent kinase 6 (CDK6) is a crucial regulator of highly aggressive AML and a recognized therapeutic target. Understanding the mechanisms initiated by CDK6 inhibition is essential to reveal therapeutic windows enabling novel combinatorial treatment strategies. We now propose to clarify the mechanism by which CDK6 regulates vesicle biogenesis and niche remodeling. We will investigate whether the combination of CDK6 inhibitors with drugs targeting vesicle biogenesis can benefit AML patients.

Approach/methods:
We will analyse the effect of CDK6 kinase-dependent and -independent functions on vesicle biogenesis and in turn niche cells with human AML cell lines and primary patient samples in combination with a 3D in vitro model and PDX mouse models. We will take advantage of human AML cell lines treated with a CDK4/6 kinase inhibitor or harboring a CDK6 C-terminally tagged degrader system to rapidly degrade endogenous CDK6 and verify CDK6 specificity. We will define how CDK6 regulates vesicle biogenesis via transcriptional regulation and protein interaction by integrating ChIP-Seq, transcriptomic and phopho-proteomic data in WP1. In WP2 we will get deeper insights if CDK6 inhibition changes the AML-EV cargo and if these changes effect niche cells by establishing a 3D model with stromal, endothelial and healthy hematopoietic cells with AML-EVs. Cells of this model will be phenotypically and functionally analysed and the transcriptomic pattern will be determined by scRNA-Seq. A combinatorial drug screen with CDK6 inhibitors and small molecules targeting vesicle biogenesis will propose novel therapeutic strategies in WP3. We will validate the results in human patient samples in vitro and in vivo.

Level of originality/innovation:
Studying communication of the malignant niche is key in understanding disease mechanisms and to define novel therapeutic strategies, especially for malignancies with limited therapeutic options. EVs are one route for cell-cell interaction and influencing their regulation might present attractive novel therapies. CDK4/6 kinase inhibitors are already in clinical use, however single treatment shows very limited success. Drug combinations with CDK4/6 kinase inhibitors to effect vesicle biogenesis and therefore the leukemic niche might lead to increased therapeutic success and open novel therapeutic windows for AML.

Primary researchers involved:
The project will be led by the applicants Karoline Kollmann and Paulo De Sepulveda. The experimental part will be mainly performed by a PostDoc and a PhD student.