Discovery of cellular dependencies and therapeutic targets in sarcoma, with a particular interest in gastrointestinal stromal tumor, dedifferentiated liposarcoma, leiomyosarcoma and Ewing sarcoma:
To identify genes and pathways contributing to sarcoma growth and survival, we are performing genome-wide functional genetic evaluations in representative sarcoma models that we have developed in the laboratory. Within a close collaboration with Jonathan Fletcher’s Laboratory and the Broad Institute, we are utilizing state-of-the-art high-throughput genetic screening technologies that functionally interrogate 16,000-18,000 genes in sarcoma cells.
We are using two complementary approaches: 1) a loss-of-function screen consisting of high-throughput RNAi-mediated gene knockdown with pooled shRNA libraries; and 2) a gain-of-function screen, using high-throughput ORF-mediated gene expression by arrayed lentiviral expression libraries. Pooled shRNA libraries were developed to perform unbiased comprehensive genetic screens, and allow for the systematic correlation of gene knockdowns with a given cellular phenotype in a high-throughput manner. We have successfully applied this technology to identify CDC37 as a more selective approach to HSP90 targeting in GIST (as published here). We have applied the same technologies to identify therapeutic targets and tumor cell dependencies in dedifferentiated liposarcoma, leiomyosarcoma, and Ewing sarcoma cell lines. We are currently in the process of analyzing and validating the promising results of these experiments.