There is an urgent need to develop novel approaches to target oncogenic transcription factors. Ewing
sarcoma (ES) is emblematic of this need. It has been known for more than 25 years that ES is absolutely
dependent on the EWS-FLI1 transcription factor for cell survival. EWS-FLI1 is the only recurrent mutation of
ES (>20% of tumors) and the dependence of the cells on this protein has been established by multiple
independent studies. Our overarching goal is to identify and clinically translate compounds that inhibit EWS-
FLI1 to improve outcomes for patients with Ewing sarcoma. Consistent with this goal, we have identified the
minor groove DNA binding compound trabectedin as an inhibitor of EWS-FLI1. We have moved this
compound into the clinic in combination with low dose irinotecan and have seen striking clinical responses.
However, some patients progress while on therapy. Other patients have required dose reductions due to
toxicity that limits the efficacy of the therapy. Therefore, in this study, we propose that a deeper understanding
of the mechanisms of activity and drug resistance will improve the therapy. We hypothesize that while these
compounds poison EWS-FLI1 by mechanisms that we have defined, they also alter chromatin structure and
cellular state in such a way that poises the cell for recovery. More precisely, we have shown that trabectedin
redistributes EWS-FLI1 in the nucleus to the nucleolus to trigger an epigenetic switch to alter chromatin
accessibility at the EWS-FLI1 driven GGAA microsatellite enhancer. However, here we propose that additional
epigenetic DNA damage response mechanisms, identified by unbiased approaches, leaves the chromatin
poised for recovery. Additionally, we have shown that redistribution of EWS-FLI1 to the nucleolus stabilizes the
fusion protein thus providing a reserve pool that facilitates transcriptional recovery. Therefore, the goal of this
study is to directly target these poised states to improve the activity of the compound, limit toxicity, and restrict
mechanisms of resistance. Importantly, these approaches should improve the toxicity profile because they
focus on EWS-FLI1 which is only found in Ewing sarcoma cells and its downstream GGAA microsatellite
enhancer which has no known function in normal cells. If successful, the study will yield a novel
mechanistically focused combination therapy for relapsed Ewing sarcoma patients that will build on the
preliminary success of trabectedin/irinotecan. In addition, the study will provide important insight into the use of
DNA binding compounds as inhibitors of oncogenic transcription factors. Finally, it will yield a novel “trapping”
approach to target phase transitioned transcription factors.
