Identification of XPO1 as a Key Molecular Vulnerability in Pediatric Atypical Teratoid/Rhabdoid Tumor (ATRT) and the Effect of Selective Nuclear Export Inhibition
Background
Atypical Teratoid/Rhabdoid Tumor (ATRT) is a fatal malignant brain tumor primarily occurring in infants under 3 years of age. The disease progresses rapidly, with an average survival period of only about one year after diagnosis. Current treatments involving high-dose chemotherapy or radiation pose risks of irreversible side effects such as brain damage and developmental delays in growing pediatric patients. Even if patients endure the harsh treatment, tumors recur easily, keeping long-term survival rates at the lowest levels.
The failure of conventional anticancer treatments stems from the disease's unique genetic defects. Instead of the complex mutations common in adult cancers, ATRT cells share a common denominator: the loss of the tumor suppressor gene SMARCB1. Given that the disease is triggered by the loss of a single tumor suppressor, it is considered extremely difficult to artificially restore the function of the already lost protein.
Due to the absence of targeted therapies, clinical practice has relied on high-dose regimens with significant risks. To overcome these limitations, it is essential to identify alternative molecular targets—genetic dependencies—that cancer cells rely on for survival. There was an urgent need to explore molecular bypasses that could precisely strike cancer cells while minimizing damage to normal cells.
Key Findings
The research team embarked on a multifaceted validation combining patient-derived ATRT cell lines, functional genomics technologies, drug screening, and transcriptome analysis. Comparative analysis of pediatric brain tumor transcriptome big data against controls revealed interesting differences. Compared with other pediatric brain tumor cell lines, ATRT cells exhibited overwhelmingly higher expression levels of the nuclear export protein Exportin-1 (XPO1). XPO1 functions as a channel that transports tumor suppressor proteins from inside the nucleus to the cytoplasm, thereby inducing their degradation.
Functional verification followed to see if ATRT cells actually depend on XPO1 for survival. When XPO1 expression was blocked using CRISPR/Cas9 gene-editing technology, cancer cell proliferation immediately halted. Similarly, administering six types of Selective Inhibitors of Nuclear Export (SINE) compounds to patient-derived cancer cells resulted in a sharp drop in cell viability. The cancer cells, deprived of their essential survival pathway, collapsed rapidly.
The anticancer mechanism of selinexor, a representative SINE-class targeted drug, has also been elucidated in detail. ATRT cells treated with selinexor ceased proliferation, remained in the quiescent G0 phase, and entered a cascade of apoptotic pathways. Transcriptomic data provided clear numerical evidence supporting this cell death process. In the drug-treated group, the TP53 signaling pathway (a tumor suppressor pathway) and apoptosis-related genes showed a steep increase, while gene sets regulating the cell cycle were simultaneously depleted. The structure shows the TP53 protein, which was being exported from the nucleus, becoming trapped inside and inducing tumor apoptosis.
Significance and Outlook
This achievement is significant because it demonstrates that XPO1 is a critical genetic dependency and a viable target supporting the survival of cells in ATRT, an intractable pediatric brain tumor. A breakthrough in identifying a new drug target in the field of rare pediatric cancers, where clear genetic drivers had remained elusive. Since selinexor has already received regulatory approval as a treatment for adult multiple myeloma, drug repurposing research is expected to gain momentum, significantly reducing development time and costs.
Several validation steps remain before actual clinical implementation. It must be further confirmed in in vivo animal models whether the drug reaches sufficient concentrations at the tumor center by crossing the blood-brain barrier (BBB). A key challenge is meticulous dose design to ensure that vulnerable infant patients can tolerate drug side effects commonly seen in adult clinical trials, such as thrombocytopenia, nausea, and fatigue. Furthermore, exploring combination therapies to block mutations in the target binding site or drug resistance that may arise during long-term administration is an essential research task.
BACKGROUND: Atypical teratoid/rhabdoid tumor (ATRT) is an aggressive central nervous system tumor mostly affecting young children. Improved and less toxic therapies for children with ATRT are imperative due to the toxicities associated with current treatments. Furthermore, existing therapies do not address the underlying genetic drivers of ATRT. In this study, we sought to determine whether exportin-1 (XPO1) is a genetic dependency and therapeutic target in ATRT. METHODS: We utilized an integrative approach harnessing patient-derived ATRT cell lines, functional genomics, pharmacologic assays, transcriptomics, and other relevant techniques. RESULTS: Analysis of RNA-sequencing datasets revealed high XPO1 expression in ATRT cells compared to other pediatric brain tumor cell lines. Both CRISPR/Cas9 genetic knockdown and pharmacologic inhibition of XPO1 using 6 selective inhibitors of nuclear export (SINEs) in patient-derived atypical teratoid/rhabdoid tumor (ATRT) cells led to significant reduction in cell viability and proliferation. Furthermore, we observed increased apoptosis, G0 phase cell cycle arrest, and upregulation of TP53 signaling pathways in cells treated with the SINE selinexor. Consistently, our transcriptomic data revealed the upregulation of apoptosis and TP53 signaling pathways and concomitant depletion of cell cycle gene sets. CONCLUSIONS: Our data reveals XPO1 as a novel genetic dependency and potent therapeutic target in ATRT.
The XPO1 inhibition strategy identified by the researchers directly leads to a customized combination therapy for pediatric patients under 3 years of age, who cannot undergo brain radiation. A representative application model is designing a clinical protocol that uses oral selinexor in combination with lower doses of standard anticancer chemotherapy. By mitigating systemic toxicity while maintaining anticancer efficacy through drug interactions, it can protect against brain developmental damage in pediatric patients. Expansion into low-dose long-term maintenance therapy to remove micro-residual tumors after surgery or prevent recurrence is also anticipated. This could lead to the establishment of a precision medicine system that selects and administers drugs to high-risk groups by measuring XPO1 expression levels in tumor tissue at the time of diagnosis.