Nuclear export inhibition shows preclinical therapeutic potential in ZFTA-RELA ependymoma
The targeted treatment gap in ependymoma and the ZFTA-RELA fusion
Inhibiting nuclear export increased the nuclear accumulation of the ZFTA-RELA fusion protein, suppressed ependymoma cell proliferation, and prolonged survival in mice. The findings suggest that even a tumor-driving protein does not necessarily favor proliferation when present at higher levels in the nucleus.
Ependymoma (EPN) is the third most common pediatric brain tumor. The paper describes maximal safe surgical resection and radiotherapy as standard treatment, with no targeted therapy available for patients. The most common tumor-driving genetic alteration in supratentorial ependymoma is a fusion of ZFTA and RELA. The fusion protein persistently localizes to the nucleus and drives tumor formation, but developing drugs that target it directly has been difficult.
A nuclear export target identified through protein interactions
The researchers used immunoprecipitation and mass spectrometry to identify proteins that interact with ZFTA-RELA. They then used a focused CRISPR-Cas9 screen to assess which of 207 genes were required for tumor cell proliferation. Comparisons with normal radial glial progenitor cells helped identify targets on which tumor cells were relatively more dependent. These candidates are proteins that could serve as therapeutic targets, not drugs themselves.
The team focused on XPO1, a nuclear export protein. They cited the ability of the XPO1 inhibitor selinexor to cross the blood–brain barrier and existing clinical experience with the drug as grounds for further development. However, prior approval by the U.S. Food and Drug Administration (FDA) does not mean that selinexor is approved to treat ependymoma.
Treatment with selinexor increased nuclear accumulation of ZFTA-RELA but did not significantly increase the expression of its target genes. The researchers suggested that target binding may already have been saturated. In patient-derived cell models, overexpressing ZFTA-RELA suppressed proliferation, whereas a mutant with defective DNA binding did not produce the same suppression. This supports the interpretation that sustained proliferation requires an appropriate level of the protein in the nucleus. All tested patient-derived cell models with ZFTA fusions had a selinexor half-maximal inhibitory concentration (IC50) below 150 nM.
Longer survival in mice and the need for clinical validation
In the patient-derived xenograft model 1425-NS, in which ZFTA-RELA drives tumor formation, selinexor monotherapy suppressed tumor growth during treatment and prolonged mouse survival. Survival improved further with a three-drug combination that added gemcitabine and ribociclib. The survival study used eight mice per group, with a one-week treatment break between two four-week treatment cycles.
These results offer clues for designing new clinical trials for ZFTA-RELA ependymoma. However, the in vivo combination effect was demonstrated in a specific patient-derived model. The researchers also noted that few ependymoma models are available and that tumor formation takes a long time, making validation across multiple models difficult. The study does not establish treatment success rates or quality-of-life improvements in patients, or the clinical safety of the three-drug combination. Efficacy and tolerability need to be assessed in follow-up clinical trials.
The methods and results are available in the original Neuro-Oncology paper.
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), 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 (i.e. Selinexor) to cross the blood brain barrier, FDA approval, and 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 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. XPO1 inhibition is an effective therapeutic strategy against ZFTA-RELA ependymoma.
Because ZFTA-RELA is difficult to block directly, the findings provide a basis for considering XPO1, which regulates the fusion protein’s nuclear abundance, as an alternative target. One possible application would be to design clinical trials of selinexor alone or in combination with gemcitabine and ribociclib for patients whose ependymoma is confirmed by molecular testing to harbor the ZFTA-RELA fusion. Existing clinical experience with these drugs may inform development, but it does not establish their efficacy in ependymoma or the safety of the three-drug combination. Moving toward evaluation in pediatric and adult patients, as proposed by the researchers, requires assessment of dose, tolerability, and tumor response. These findings constitute preclinical evidence identifying a target and combination for further testing.