Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma
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 un...
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BMC
2025-06-01
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| Series: | Acta Neuropathologica Communications |
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| Online Access: | https://doi.org/10.1186/s40478-025-02068-y |
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| author | Benjamin Lin Abigail K. Shelton Erin Smithberger Julia Ziebro Kasey R. Skinner Ryan E. Bash Richard Kirkman Allie Stamper Madison Butler Alex Flores Steven P. Angus Michael P. East Timothy F. Cloughesy David A. Nathanson Michael E. Berens Jann N. Sarkaria Zev A. Binder Donald M. O’Rourke Timothy C. Howton Brittany N. Lasseigne Christopher D. Willey Gary L. Johnson Anita B. Hjelmeland Frank B. Furnari C. Ryan Miller |
| author_facet | Benjamin Lin Abigail K. Shelton Erin Smithberger Julia Ziebro Kasey R. Skinner Ryan E. Bash Richard Kirkman Allie Stamper Madison Butler Alex Flores Steven P. Angus Michael P. East Timothy F. Cloughesy David A. Nathanson Michael E. Berens Jann N. Sarkaria Zev A. Binder Donald M. O’Rourke Timothy C. Howton Brittany N. Lasseigne Christopher D. Willey Gary L. Johnson Anita B. Hjelmeland Frank B. Furnari C. Ryan Miller |
| author_sort | Benjamin Lin |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-e53627e0de284e9085d8f86319139956 |
| institution | Kabale University |
| issn | 2051-5960 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
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| series | Acta Neuropathologica Communications |
| spelling | doaj-art-e53627e0de284e9085d8f863191399562025-08-20T03:27:13ZengBMCActa Neuropathologica Communications2051-59602025-06-0113111710.1186/s40478-025-02068-yIdentifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastomaBenjamin Lin0Abigail K. Shelton1Erin Smithberger2Julia Ziebro3Kasey R. Skinner4Ryan E. Bash5Richard Kirkman6Allie Stamper7Madison Butler8Alex Flores9Steven P. Angus10Michael P. East11Timothy F. Cloughesy12David A. Nathanson13Michael E. Berens14Jann N. Sarkaria15Zev A. Binder16Donald M. O’Rourke17Timothy C. Howton18Brittany N. Lasseigne19Christopher D. Willey20Gary L. Johnson21Anita B. Hjelmeland22Frank B. Furnari23C. Ryan Miller24Medical Scientist Training Program, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamDepartment of Biology, University of North CarolinaUniversity of North Carolina School of MedicineDepartment of Pediatrics, Indiana University School of MedicineDepartment of Pharmacology, University of North Carolina School of MedicineDepartment of Neurology, David Geffen School of Medicine, University of California, Los AngelesDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los AngelesCancer and Cell Biology Division, Translational Genomics Research InstituteDepartment of Radiation Oncology, Mayo ClinicDepartment of Neurosurgery and Glioblastoma Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine, University of PennsylvaniaDepartment of Neurosurgery and Glioblastoma Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine, University of PennsylvaniaDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at BirminghamDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at BirminghamO’Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at BirminghamDepartment of Pharmacology, University of North Carolina School of MedicineDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at BirminghamDepartment of Medicine, Division of Regenerative Medicine, University of California, San DiegoDivision of Neuropathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamAbstract 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.https://doi.org/10.1186/s40478-025-02068-yEGFRGlioblastomaSynthetic lethalityKinome rewiringUpfront combinatorial therapy |
| spellingShingle | Benjamin Lin Abigail K. Shelton Erin Smithberger Julia Ziebro Kasey R. Skinner Ryan E. Bash Richard Kirkman Allie Stamper Madison Butler Alex Flores Steven P. Angus Michael P. East Timothy F. Cloughesy David A. Nathanson Michael E. Berens Jann N. Sarkaria Zev A. Binder Donald M. O’Rourke Timothy C. Howton Brittany N. Lasseigne Christopher D. Willey Gary L. Johnson Anita B. Hjelmeland Frank B. Furnari C. Ryan Miller Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma Acta Neuropathologica Communications EGFR Glioblastoma Synthetic lethality Kinome rewiring Upfront combinatorial therapy |
| title | Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma |
| title_full | Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma |
| title_fullStr | Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma |
| title_full_unstemmed | Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma |
| title_short | Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma |
| title_sort | identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of egfrviii driven glioblastoma |
| topic | EGFR Glioblastoma Synthetic lethality Kinome rewiring Upfront combinatorial therapy |
| url | https://doi.org/10.1186/s40478-025-02068-y |
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