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. Upfront combinatorial therapy featuring EGFR tyrosine kinase inhibitors (TKI) may overcome these challenges. To identify combinatorial drug targets within the kinome, we temporally characterized drug-induced kinome rewiring in isogenic, genetically engineered Cdkn2a-deleted mouse astrocytes expressing human EGFRvIII. We utilize RNA sequencing and multiplex inhibitor beads, coupled with mass spectrometry, to demonstrate that kinome rewiring exhibits both shared and unique kinases after acquired resistance develops to EGFR TKI, despite using models with a common genetic background. Additionally, we noted that kinases altered in the acute setting are distinct from those in acquired resistance. By identifying kinome vulnerabilities throughout the acute, dynamic drug response process, we generated a kinase signature associated with EGFR inhibition. Further molecular interrogation of signature genes revealed that drug treatment induces an unexpected increase in Cdk6 protein, but not mRNA, despite live cell imaging and transcriptomic evidence indicating decreased proliferation. Survival experiments with orthotopic allografts show that upfront combination inhibition of Cdk6, using abemaciclib, and EGFR, using 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.

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Publication Details

Journal
Acta Neuropathologica Communications
Published
2025-06-28
DOI
https://doi.org/10.1186/s40478-025-02068-y
Primary Topic
Protein Degradation and Inhibitors
Type
article
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0.00

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article

Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma

Erin Smithberger, David A. Nathanson, Timothy C. Howton, Kasey Skinner et al.
Acta Neuropathologica Communications
Protein Degradation and Inhibitors
article

Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma

Erin Smithberger, David A. Nathanson, Timothy C. Howton, Kasey Skinner, Jann Nagina Sarkaria, Ryan Bash, Zev A. Binder, Frank B. Furnari, Anita B. Hjelmeland, Gary L. Johnson, C Ryan Miller, Michael E. Berens, Madison Butler, Timothy F. Cloughesy, Julia Ziebro, Christopher D. Willey, Steven P. Angus, Brittany N. Lasseigne, Richard Kirkman, Allie Stamper, Donald M. O’Rourke, Michael P. East, Abigail Shelton, Benjamin Lin, Álex Flores
article en

Abstract

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. Upfront combinatorial therapy featuring EGFR tyrosine kinase inhibitors (TKI) may overcome these challenges. To identify combinatorial drug targets within the kinome, we temporally characterized drug-induced kinome rewiring in isogenic, genetically engineered Cdkn2a-deleted mouse astrocytes expressing human EGFRvIII. We utilize RNA sequencing and multiplex inhibitor beads, coupled with mass spectrometry, to demonstrate that kinome rewiring exhibits both shared and unique kinases after acquired resistance develops to EGFR TKI, despite using models with a common genetic background. Additionally, we noted that kinases altered in the acute setting are distinct from those in acquired resistance. By identifying kinome vulnerabilities throughout the acute, dynamic drug response process, we generated a kinase signature associated with EGFR inhibition. Further molecular interrogation of signature genes revealed that drug treatment induces an unexpected increase in Cdk6 protein, but not mRNA, despite live cell imaging and transcriptomic evidence indicating decreased proliferation. Survival experiments with orthotopic allografts show that upfront combination inhibition of Cdk6, using abemaciclib, and EGFR, using 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.

Acta Neuropathologica CommunicationsVol. 13(1)
University of North Carolina at Chapel Hill (US), Translational Genomics Research Institute (US), University of California, Los Angeles (US), University of Alabama at Birmingham (US), University of California San Diego (US), Mayo Clinic in Arizona (US), Translational Therapeutics (United States) (US), Indiana University School of Medicine, Indiana University – Purdue University Indianapolis (US), University of Pennsylvania (US)
National Science Foundation, Heflin Center for Genomic Science, University of Alabama at Birmingham, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Neurological Disorders and Stroke
Good health and well-being
Openalex Percentile: Top 86%
Protein Degradation and Inhibitors
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