CDK8 as a New Therapeutic Target in Alveolar Rhabdomyosarcoma
Treatment options for children with fusion-driven Alveolar Rhabdomyosarcoma (aRMS) are very limited, and there are no approved new targeted therapy approaches for these children. In fact, there have been no substantial improvements in treatments for these children in over two decades. I have identified CDK8 as a candidate therapeutic target in aRMS and interaction partner of PAX3-FOXO1, the abnormal gene involved in the initiation and maintenance of this disease. Completion of these proposed studies is impactful because these studies will both determine the mechanisms by which aRMS is dependent on CDK8 for disease maintenance and validate this target in preclinical models of aRMS. Furthermore, the proposed studies will use unbiased approaches to identify new drug combinations and mechanisms of resistance to CDK8 inhibitors in aRMS setting the stage for future second-generation clinical trials. Clinical grade inhibitors of CDK8 are commercially available and in early phase studies in the clinic for other diseases. Thus, if successful, this project will inform a clinical trial testing a CDK8 inhibitor in patients with fusion-positive aRMS.
Project Goal:
Alveolar Rhabdomyosarcoma (aRMS) is one of the most difficult-to-treat childhood cancers with poor overall survival and little change in treatment over the past two decades. To improve the outcome of children with this aggressive cancer, new targeted therapies must be identified, validated in preclinical models, and ultimately translated to clinical trial. This proposal focuses on fusion-positive aRMS, typically driven by abnormal genes called PAX3-FOXO1 or PAX7-FOXO1. While direct targeting of this kind of genes is quite challenging, an alternative approach would be to target their interaction partners. In the case of aRMS, I identified a selective dependency on CDK8, a kinase involved in transcription and recruited by PAX3-FOXO1, through the analysis of genome-scale CRISPR-Cas9 screening data. In this proposal, in Aim 1 I will perform assays to examine the effects of CDK8 inhibition on aRMS cell phenotypes (e.g., growth, cell cycle, and cell death) using both genetic and chemical approaches. In addition, aRMS cell line and patient-derived xenografts will be used to evaluate how CDK8 inhibition affects tumor growth in preclinical models. Aim 2 will determine the transcriptional and epigenetic consequences of CDK8 inhibition in aRMS with the hypothesis that CDK8 inhibition will alter PAX3-FOXO1 localization on chromatin. The studies of this aim will begin with RNA sequencing to examine the acute and chronic impact of inhibiting CDK8 on transcription. Furthermore, assays will be performed to determine the impact of CDK8 inhibitors on PAX-FOXO fusion localization on chromatin, chromatin accessibility, 3D chromatin architecture, and histone marks that indicate enhancer and promoter activity. Aim 3 will explore CDK8 inhibition-based therapeutic combinations. Here, I will conduct a genome-scale CRISPR-Cas9 screen to identify genes that when deleted lead to either an enhanced response or resistance to CDK8 inhibition in aRMS models. Hits will be validated with genetic and degrader approaches, and with small molecule inhibitor approaches when feasible. This proposal will uncover both the mechanistic role of CDK8 in aRMS and its potential as a therapeutic target for children with this poorly treated pediatric malignancy.
