Identifying and Exploiting Combinatorial Synthetic Lethality by Characterizing Adaptive Kinome Rewiring of EGFRvIII-driven Glioblastoma

GBM is an aggressive primary malignant brain tumor that has a poor prognosis. Molecular characterization of GBM has shown that EGFR mutations are present in over 50% of tumors. However, EGFR inhibitors have not shown clinical efficacy in contrast to other EGFR-driven neoplasms due to the unique EGFR biology found in GBM. We believe that upfront combinatorial therapy with EGFR inhibitors can overcome these challenges. To identify combinatorial drug targets, we temporally characterized drug induced EGFRvIII kinome rewiring in a cell line with an isogenic genetically engineered GBM EGFRvIII kinome. Kinomic characterization show that kinome rewiring has both shared and unique kinases after acquired resistance develops despite a common genetic origin. Additionally, we noted that the kinases altered in the acute setting are distinct from those in acquired resistance. By identifying these differential temporal kinomic vulnerabilities throughout the drug response process, we generated a kinase signature associated with inhibition of EGFR. Further molecular interrogation of these signature genes reveals that drug treatment induces an unexpected increase in Cdk6 protein but not mRNA despite a decrease in proliferation measured by both live cell counts and transcriptomics. Survival experiments with two cohorts of orthotopic allografts show that upfront combination inhibition of Cdk6, with abemaciclib, and EGFR, with neratinib, significantly prolonged median survival compared to neratinib alone. Our findings suggest that identifying and inhibiting targets with synthetic lethality in the upfront combinatorial setting is a viable approach for precision oncology and may help provide an avenue to overcome the resistance mechanisms that contributed to the failures of EGFR as a molecular target in GBM. Here we performed transcriptomic charecterization of an isogenic genetically engineered EGFRvIII kinome after treatment with EGFR TKI. Transcritomics was performed at 0, 4, 24, and 48 after treatment and also after acquired resistance developes.