Genetic Screen in a Pre-Clinical Model of High-Grade Complex Karyotype Sarcoma Characterizes Drivers of Distinct Sarcoma Subtypes and Identifies New Therapeutic Vulnerabilities
Authors: Freeland Jack , Muñoz Maria , O’Donnell Edmond , Langerman Justin , Bergonio Jessica , Suarez-Navarro Julissa , Darrow Morgan , Thorpe Steven , Canter Robert , Randall R. Lor , Plath Kathrin , Carraway Kermit , Witte Owen N. , Graeber Thomas G. , Carr-Ascher Janai R. 
Published: June 2022

High-grade complex karyotype sarcomas are a heterogeneous group of more than seventy tumors that vary in histology, clinical course, and patient demographics. Despite these clear differences, these high-grade sarcomas are treated similarly with a uniformly high metastatic rate. Pre-clinical models that allow for rigorous comparisons of distinct human sarcoma subtypes would advance insights into the relationships between sarcomas and inform therapeutic decisions. We describe the robust transformation of human mesenchymal stem cells into multiple subtypes of high-grade sarcoma. Using a pooled genetic screening approach, we identified key drivers and potential modifiers of transformation.YAP1andKRASwere validated as drivers of two distinct sarcoma subtypes, undifferentiated pleomorphic sarcoma (UPS) and myxofibrosarcoma (MFS), respectively. In addition, the pathology of tumors driven byCDK4andPIK3CAreflected leiomyosarcoma (LMS) and osteosarcoma (OS) indicating that further iterations of this model could result in additional sarcoma subtypes. Histologically and phenotypically these tumors reflect human sarcomas including the pathognomonic complex karyotype. In addition,CDK4andPIK3CAdriven tumors demonstrated endogenousYAP1amplification which is seen across a subset of human tumors. While all tumors overlapped transcriptionally with the TCGA sarcoma data, further analysis confirmed thatYAP1andKRAStumors recapitulate the UPS and MFS subtypes. Co-analysis of TCGA and model tumors support that these sarcoma subtypes lie along a spectrum of disease and adds guidance for further transcriptome-based refinement of sarcoma subtyping. Within complex karyotype sarcomas, there are multiple genetic changes but identifying those that are clinically relevant has been challenging. Comparing differentially expressed genes inYAP1andKRAStumors to human UPS and MFS identified the enrichment of oxidative phosphorylation pathways in bothYAP1tumors and UPS. Treatment of a panel of sarcoma cell lines with the combination of an oxidative phosphorylation inhibitor and Hippo pathway inhibitor led to a significant impairment in growth identifying new therapeutic targets. A subset of human UPS tumors showed an even greater enrichment in these pathways indicating this model can be used to identify clinically relevant subtypes. This model can be used to begin to understand pathways and mechanisms driving human sarcoma development, the relationship between sarcoma subtypes and to identify and test new therapeutic vulnerabilities for this aggressive and heterogeneous disease.

Statement of Significance

We have created the first model to study the development, growth, and metastasis of multiple human sarcoma subtypes. This system can be used as a platform to investigate sarcoma biology and identify new therapeutic targets across a heterogeneous disease.