PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas

Abstract

Background: Glioma is the most common intrinsic brain tumor and also occurs in the spinal cord. Activating EGFR mutations are common in IDH1 wild-type gliomas. However, the cooperative partners of EGFR driving gliomagenesis remain poorly understood. Results: We explore EGFR-mutant glioma evolution in conditional mutant mice by whole-exome sequencing, transposon mutagenesis forward genetic screening, and transcriptomics. We show mutant EGFR is sufficient to initiate gliomagenesis in vivo, both in the brain and spinal cord. We identify significantly recurrent somatic alterations in these gliomas including mutant EGFR amplifications and Sub1, Trp53, and Tead2 loss-of-function mutations. Comprehensive functional characterization of 96 gliomas by genome-wide piggyBac insertional mutagenesis in vivo identifies 281 known and novel EGFR-cooperating driver genes, including Cdkn2a, Nf1, Spred1, and Nav3. Transcriptomics confirms transposon-mediated effects on expression of these genes. We validate the clinical relevance of new putative tumor suppressors by showing these are frequently altered in patients' gliomas, with prognostic implications. We discover shared and distinct driver mutations in brain and spinal gliomas and confirm in vivo differential tumor suppressive effects of Pten between these tumors. Functional validation with CRISPR-Cas9-induced mutations in novel genes Tead2, Spred1, and Nav3 demonstrates heightened EGFRvIII-glioma cell proliferation. Chemogenomic analysis of mutated glioma genes reveals potential drug targets, with several investigational drugs showing efficacy in vitro. Conclusion: Our work elucidates functional driver landscapes of EGFR-mutant gliomas, uncovering potential therapeutic strategies, and provides new tools for functional interrogation of gliomagenesis.

Slc1a3-2A-CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and effectors in the 129S4 genetic background

“…Therefore, selective vulnerability to neurodegenerative disease, the concept where specific brain regions are most severely targeted in a disease-specific pattern is not simply determined by expression www.nature.com/scientificreports/ patterns of the disease-causing proteins 97 . Beyond neurodegenerative diseases, this mouse line may prove useful in other fields of biomedical research, for example in vivo screens of glioma 98,99 . Finally, we thought it would be interesting to compare the translatomes of B6 and S4 mice using the same Slc1a3-2A-CreERT2 construct.…”

Anti-PD-1 Immunotherapy in Preclinical GL261 Glioblastoma: Influence of Therapeutic Parameters and Non-Invasive Response Biomarker Assessment with MRSI-Based Approaches

“…It may be relevant to evaluate in future work whether less immunogenic models respond to IMS combined TMZ/anti PD-1, like the CT-2A model [ 44 ]. Moreover, other authors favour genetically engineered mice (GEM) models of GB, harbouring defined driver mutations leading to tumour progression [ 45 , 46 , 47 ], which are claimed to better reproduce human GB development. We hope the robustness of our treatment strategy and the MRSI-based biomarker used for the detection of its efficiency can be put to test also in GEM models of GB by our team or by other groups in the field.…”

Metabolic Alterations Related to Glioma Grading Based on Metabolomics and Lipidomics Analyses

“…The research studies initiated by IDH could provide potential strategies for glioma treatment and prognosis. Recently, Noorani et al explored the role of EGFR mutants in IDH1 wild-type gliomas through whole-exome sequencing, transcriptomics and transposon mutagenesis forward genetic screening, and found new putative tumor suppressors [8]. There are many studies of this kind, starting with genes, which have contributed to the field of glioma.…”