Functional discovery of targetable dependencies in recurrent glioblastoma (original) (raw)

2022, Research Square (Research Square)

Resistance to genotoxic therapies and tumor recurrence are hallmarks of glioblastoma (GBM), an aggressive brain tumor. Here, we explore the functional drivers of post-treatment recurrent GBM. By conducting genome-wide CRISPR-Cas9 screens in patient-derived GBM models, we uncover distinct genetic dependencies in recurrent tumor cells that were absent in their patient-matched primary predecessors, accompanied by increased mutational burden and differential transcript and protein expression. These analyses map a multilayered genetic response to drive tumor recurrence, identifying protein tyrosine phosphatase 4A2 (PTP4A2) as a novel modulator of self-renewal, proliferation and tumorigenicity at GBM recurrence. Mechanistically, genetic perturbation or small molecule inhibition of PTP4A2 represses axon guidance activity through a dephosphorylation axis with roundabout guidance receptor 1 (ROBO1), exploiting a functional dependency on ROBO signaling. Importantly, engineered anti-ROBO1 single-domain antibodies also mimic the effects of PTP4A2 inhibition. We conclude that functional reprogramming drives tumorigenicity and dependence on a multi-targetable PTP4A2-ROBO1 signaling axis at GBM recurrence. Full Text For decades, clinicians have administered radiation therapy and chemotherapy to treat cancer patients 1. In parallel, resistance to these genotoxic treatments and tumor recurrence have become an inevitable reality for aggressive tumors. However, despite the clinical relevance and applications, functional drivers of disease recurrence remain poorly understood. Glioblastoma (GBM) remains the most aggressive and prevalent malignant primary brain tumor in adults 2. Unchanged since 2005, standard of care (SoC) consists of surgical resection, followed by radiation therapy (RT) plus concurrent and adjuvant chemotherapy with temozolomide (TMZ) 3,4. Despite these therapeutic efforts, patients inevitably succumb to recurrent disease with a median overall survival of 14.6 months and a ve-year survival rate of 5.5-6.8% 2,3,5. Unbiased genome-wide functional genomic screens have provided insights into genes and pathways regulating tumor cell survival, invasion, and sensitivity to TMZ in primary pre-treatment tumor cells 6-9. However, these studies do not examine changes at post-treatment tumor recurrence, and thus cannot explain treatment failure in ~70% of GBM patients 10. Here, we conduct a genome-scale comparison between patient-matched pre-and post-treatment GBM cells at the functional, transcriptomic, and proteomic levels. We uncover a therapeutic vulnerability for protein tyrosine phosphatase 4A2 (PTP4A2) at tumor recurrence, and introduce a modulatory role for PTP4A2 on axonal guidance proteins. Comparing primary and recurrent GBM We derived a pair of patient-matched GBM cell lines, one from a tumor specimen obtained at initial diagnosis prior to chemoradiotherapy (BT594, primary tumor cells), and a second specimen obtained at rst disease recurrence post-therapy (BT972, recurrent tumor cells) (Figure 1A, Table S1). Consistent with previous observations 11,12 , recurrent tumor cells showed a 25-fold increase in in vitro self-renewal capacity (P = 5.0e-09