Abstract Resistance to genotoxic therapies and subsequent disease recurrence are hallmarks of aggressive cancers, including glioblastoma (GBM). Here, we uncover functional drivers of post-treatment recurrent GBM using genome scale CRISPR-Cas9 screens accompanied by integrative genomic analysis. Using patient-matched pre- and post-treatment GBM models, our findings uncover large-scale reorganization of functional dependencies at tumor recurrence and implicate protein tyrosine phosphatases 4A2 (PTP4A2) as a novel driver of tumorigenicity in recurrent GBM. Small molecule inhibition and phospho-proteomic analyses reveal a novel PTP4A-ROBO1 signaling axis that modulates tumor invasion, self-renewal and proliferation in recurrent GBM. Since a pan-PTP4A targeting small molecule suffers from poor blood-brain-barrier penetrance, we engineered a novel second generation chimeric antigen receptor (CAR) targeting human ROBO1, a cell surface receptor enriched across GBM specimens. Not only do ROBO1 CAR T cells exhibit a potent and specific anti-tumor effect in vitro, a single dose of ROBO1 CAR T cells doubles median survival in a patient-derived xenograft (PDX) model of recurrent GBM. Expansion of ROBO1 CAR T cells to other invasive brain cancers leads to tumor eradication in ~50% of mice in PDX models of pediatric medulloblastoma and adult lung-to-brain metastases. Together, we provide insights into functional remodeling of GBM at recurrence and present a multi-targetable PTP4A-ROBO1 signaling axis with potential across multiple malignant brain tumors.
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