Probing Synovial Sarcomas and the Ubiquitin-Proteasome System With Small Molecules

Abstract

Chemical probes have radically transformed our ability to modulate cellular activity by providing robust and reversible disruption of select biological processes. To uncover a novel set of these tools, I first performed a small molecule screen to identify compounds that could selectively prevent the growth of synovial sarcoma (SS) cell lines and observed that MET inhibitors could target a distinct subset. This MET sensitivity was defined by amplification of the MET gene and an active AKT pathway. Through immunohistochemistry of SS patient tumor samples, I discovered that MET is only expressed in the glandular component of biphasic SS, the same histological subtype of the SS cell lines that were sensitive to MET inhibition. Furthermore, this dependency could be targeted in vivo, with the MET inhibitor SGX-523 preventing the growth of a biphasic SS xenograft in mice. I also compared the transcriptional changes caused by MET inhibition to loss of SS18-SSX1, the fusion protein understood to initiate SS oncogenesis. These two perturbations were found to behave very similarly, altering pathways associated to the epithelial to mesenchymal transition, cell-cycle progression, and differentiation. This is one of the first targetable dependencies discovered in this cancer and it could have a marked impact in the future of SS treatment. Second I executed a screen to identify compounds that could increase the protein levels of the tumor suppressor BAF47 in SS cells and discovered BRD1732, a novel probe of the ubiquitin-proteasome pathway with a novel mechanism of action (MOA) and a yet to be identified target. Cellular treatment with BRD1732 causes a profound increase in the levels of free cellular ubiquitin alongside various protein level increases (e.g. of p21/p27), inhibition of NFκB signaling, and inhibition of the unfolded protein response. The compound does not inhibit the human 26S proteasome, E1 or most E2 enzymes in vitro, suggesting a unique MOA distinct from canonical proteasome inhibition. BRD1732 can also prevent the growth of various cancer cell lines, indicating a potential for translation into the clinic. This probe could uncover novel biology surrounding protein homeostasis and further the therapeutic relevance of the ubiquitin-proteasome pathway.