Nuclear export as a therapeutic vulnerability in ZFTA-RELA ependymoma

Abstract Background Ependymoma (EPN) is the third most common pediatric brain tumor with no targeted therapies available to patients. In supratentorial ependymoma, the most frequent driver alteration is a gene fusion between ZFTA and RELA (denoted ZR), which leads to constitutive localization of ZR in the nucleus. Because ZR is not currently druggable, we tested whether ZR expression leads to aberrant protein interactions that could represent therapeutic vulnerabilities. Methods Using CRISPR-Cas9 pooled screening, we identified many novel druggable ZR-interacting proteins including XPO1, CARM1, SMARCA4, and CDK1. We focused on the nuclear export protein (XPO1), given the ability of most XPO1 inhibitors (ie, selinexor) to cross the blood-brain barrier, FDA approval, and have documented safety profiles in children. Results We found that specific nuclear ZR levels are needed for cell proliferation and are regulated by XPO1. Increased ZR accumulation in the nucleus does not increase oncogenic gene expression but drives tumor cells out of the cell cycle, as compared to a defective ZR DNA-binding mutant. Treatment of ZR-driven patient-derived mouse models with selinexor impairs cell growth and extends survival of animals in vivo. The combination of selinexor treatment with gemcitabine and ribociclib (used in a clinical trial for relapsed EPN at St. Jude Children’s Research Hospital [SJDAWN]) further extends mouse survival. Conclusion Our findings demonstrate that ZR-interacting proteins constitute therapeutic leads and that XPO1 is critical for titrating “goldilocks” levels of ZR nuclear expression. We identify a novel combination therapy of selinexor, gemcitabine, and ribociclib that may be immediately translated into clinical trials for EPN patients that are currently without targeted treatments.