Connecting Genomic Alterations in Liposarcomas with Drug Responses and Identification of New Therapeutic Approaches

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PROJECT SUMMARY Approximately 12,000 individuals in the USA will develop soft tissue sarcoma in 2015. In adults, liposarcoma (LPS) is one of the most common types of soft tissue sarcoma. Though rare, LPS tumors are often very aggressive with high morbidity and mortality rates. Resistance to conventional chemotherapeutics and lack of effective targeted therapies create a critical need to develop novel treatment options for patients with this devastating disease. Recent large-scale analyses by us and other groups have provided a comprehensive view of the genomic landscape of LPS. Despite the new insights, these studies, for the most part have not translated into definitive therapeutic strategies. One challenge is determining how individual gene -drug relationships affect drug responses ; a second challenge is that many of the genetic alterations identified in LPS have not been paired to a suitable targeted therapy. Synthetic lethality is an attractive approach for selective therapeutic targeting of cancer cells lacking otherwise obvious actionable genetic vulnerabilities. Large-scale cancer cell line screens helped uncover synthetic lethal interactions that link genetic determinants to drug responses; yet due to the complexity of most cancer cell lines, distinguishing the relevance of single mutations to the impact of a drug remains difficult. In the current proposal we will use an innovative approach to address these challenges. Our aim is to link specific LPS associated genetic alterations with sensitivities to multiple clinically relevant compounds. Thus, our study will begin to bridge the gap between the plethora of genetic alterations that we and others identified in LPS genomes and clinical implementation. We will use a novel screening strategy based on partly transformed mesenchymal stem cells (MSC) which we will genetically engineer to express a series of specific, recurrent LPS genotypic alterations. The resulting panel of isogenic clones and parental control cells will be subjected to high-throughput small molecule and siRNA screens (Collaboration with Dr. J. Tyner, Oregon University, Portland, and Sanford Burnham, La Jolla). Results will be validated and functionally investigated in LPS cell lines and animal models. In addition, we will perform a cutting-edge, genome-wide CRISPR screen to identify drugs that synergize with a leading compound that we will identify in our initial screens. Impact: We will conduct an integrative analysis of drug sensitivities p athway alterations and genotype-specific dependencies in a panel of isogenic MSC clones; results are likely to uncover previously unexpected gene-drug interactions that will allow us to nominate actionable therapeutic targets and suggest combinational treatments to mitigate drug resistance. Ultimately, our study will help guide new clinical trials for various investigational and help develop new genotype- , FDA-approved and drugs, directed therapies for subsets of LPS patients currently lacking satisfactory therapeutic options.