A novel combination of CDK4/6 and PI3K inhibitors exhibits highly synergistic activity and translational potential in Ewing sarcoma.

Abstract

Ewing sarcoma is a highly aggressive solid malignancy affecting children and young adults. Ewing sarcoma is driven primarily by EWSR1::FLI1, a fusion oncoprotein that has been notoriously difficult to target with traditional pharmacologic agents. There are numerous examples of preclinical promising combinations of small molecules that are never tested in pediatric clinical trials because agents fail to reach the market due to limited efficacy for common adult cancers. Moreover, the effectiveness of single-agent therapies for cancer treatment is often limited. To address these limitations, we selected 28 compounds that were largely FDA approved or in late stages of clinical development and known to regulate important pathways in Ewing sarcoma. We performed a drug screen in Ewing sarcoma cell lines with 180 combinations of tyrosine kinase inhibitors, cell cycle inhibitors, and conventional chemotherapy. The results of the screen revealed that a PI3K inhibitor, copanlisib, combined with a CDK4/6 inhibitor, ribociclib, exhibited strong synergistic anti-Ewing sarcoma activity. Using proteomic methods such as a reverse-phase protein array and western immunoblotting, we demonstrated that this combination induced a downregulation of the PI3K/AKT pathway as well as proteins involved in cell cycle regulation. We further confirmed these in vitro data using bulk RNA-sequencing. To evaluate the phenotypic effect of the PI3K/CDK4/6 inhibition in Ewing sarcoma lines, we performed apoptosis and cell cycle analyses using flow cytometry and demonstrated that ribociclib primarily induced a G0/G1 arrest with minimal effect on Ewing cell viability but significantly enhanced the apoptotic effect of copanlisib treatment. In a xenograft model of Ewing sarcoma, we demonstrated that the combination therapy significantly prolonged survival compared to treatment with either vehicle or single-agent therapy alone. Our findings identify a new candidate therapy combination for Ewing sarcoma using FDA-approved drugs and provide a resource of additional potential synergistic combinations for future validation. Statement of translational relevanceTreatment of patients with newly diagnosed Ewing sarcoma involves intensive multi- agent chemotherapy, radiation, and surgery, often leading to long-term toxicities. Children with relapsed or metastatic disease experience poor outcomes with five-year overall survival rates of only 15 to 30 percent. Therefore, new therapeutic approaches are urgently needed. Our drug screen revealed several promising combinations with synergistic anti-Ewing sarcoma activity including the PI3K inhibitor copanlisib with the CDK4/6 inhibitor ribociclib. This combination also significantly improved survival in a mouse xenograft model of Ewing sarcoma compared to treatment with vehicle or either drug alone. Pre-clinical validation of a combination therapy composed of two FDA- approved drugs nominates this combination for early phase trials for patients with with relapsed or refractory Ewing sarcoma, a group of patients greatly in need of new therapeutic opportunities. The data generated by our drug screen may also be used as a resource to identify other promising combinations for future validation as Ewing sarcoma therapies.