Leveraging Medulloblastoma Clonal Dynamics to Overcome Treatment Resistance

Medulloblastoma is a common pediatric brain tumor with distinct molecular subgroups. Among them, group 3 medulloblastoma is associated with increased recurrence, metastatic potential, and poor patient outcomes. Small-molecule inhibitors targeting B cell-specific Moloney murine leukemia virus insertion site 1 (BMI1) have demonstrated efficacy against several types of malignant tumors, including pediatric medulloblastoma. Although our previously published in vivo study provided a promising proof of concept for the therapeutic targeting of BMI1 in group 3 medulloblastoma with small-molecule inhibitors, it is not sufficient to eradicate the tumor.

In this study, following preclinical validation of BMI1 inhibitor PTC596, DNA barcoding technology was leveraged to profile in vivo clonal dynamics of group 3 medulloblastoma in response to the established chemoradiotherapy regimen alone and in combination with PTC596. Following demonstration of a small number of treatment-refractory clones, we sought to identify potential druggable molecular vulnerabilities by utilizing phosphoproteomic profiling and genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screening.

By comparing the changes in the phosphorylation pattern of key signaling kinases after PTC596 treatment with the list of sensitizer genes from in vitro genome-wide CRISPR/CRISPR-associated protein 9 screen and with the essential genes in human neural stem cells, we identified several context-specific regulators of mTOR, AKT, and PLK1 pathways. Subsequently, targeting the PI3K pathway with enzastaurin was most amenable to synergistic targeting alongside BMI1 inhibition.

This work provides the foundation for clinical validation of small-molecule inhibitors synergistic with PTC596 to improve the durability of remissions and extend the survival of patients with treatment-refractory group 3 medulloblastoma.