ATRT-03. Targeting nuclear export as a potent therapeutic strategy in atypical teratoid/rhabdoid tumors

Abstract Background Atypical teratoid/rhabdoid tumor (AT/RT) is an aggressive brain cancer that mostly affects children under age 3. While there have been some improvements in outcomes with multimodal therapy, there remains significant treatment-related toxicities associated with intensive therapy. Thus, improved and less toxic therapies for children with AT/RT are necessary. One strategy to determine novel therapeutic approaches is through the identification of cancer dependencies. Exportin-1 (XPO1) is a nuclear export protein that transports cargo proteins containing a nuclear export signal from the nucleus to the cytoplasm. In other cancers, elevated XPO1 expression has been associated with poor prognosis. Methods We harnessed an integrative approach using functional genomics, in vitro AT/RT models, transcriptomics, drug assays, and in vivo intracranial xenograft models to systematically test the hypothesis that XPO1 is a therapeutic vulnerability in AT/RT. Results Analysis of RNA-sequencing data across pediatric brain tumor cell lines demonstrates that XPO1 is highly expressed in AT/RT cells. Genetic knockdown of XPO1 using CRISPR-Cas9 in patient-derived AT/RT cells led to profound defects in cell viability and proliferation. Pharmacologic inhibition of XPO1 using six different XPO1 inhibitors in multiple AT/RT cell lines showed as low as 5.05 nM IC50. XPO1 inhibition led to significant apoptosis and on target degradation of XPO1 protein levels. Transcriptomic analysis of AT/RT cells with genetic and pharmacologic inhibition of XPO1 is currently underway. Furthermore, we are harnessing protein fractionation coupled with mass spectrometry to specifically identify XPO1 cargo proteins. Additionally, we have tested combinatorial approaches with gemcitabine and XPO1 inhibition to evaluate synergistic effects. Lastly, we are testing this combination using intracranial xenograft murine models of AT/RT to assess in vivo effects on overall survival. Therefore, we demonstrate that XPO1 is a dependency in AT/RT, and targeting nuclear export in combination with cytotoxic chemotherapy shows high translational potential.