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

Title
PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas
Authors
Noorani, Imrande, la Rosa JorgeChoi, Yoon HaStrong, AlexanderPonstingl, HannesVijayabaskar, M.S.Lee, Ju SungLee, Eun MinRichard-Londt, AngelaFriedrich, MathiasFurlanetto, FedericaFuente, RocioBanerjee, RubyYang, FengtangLaw, FrancesWatts, ColinRad, RolandVassiliou, GeorgeKim, Jong KyoungSantarius, ThomasBrandner, SebastianBradley, Allan
DGIST Authors
Lee, Eun Min; Kim, Jong Kyoung
Issue Date
2020-07
Citation
Genome Biology, 21(1), 181
Type
Article
Article Type
Article
Keywords
GROWTH-FACTOR-RECEPTORINTEGRATED GENOMIC ANALYSISSPINAL-CORD TUMORSNEURAL STEM-CELLSSLEEPING-BEAUTYTRANSPOSON MUTAGENESISADJUVANT TEMOZOLOMIDEREAD ALIGNMENTCANCERGLIOBLASTOMA
ISSN
1474-760X
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. © 2020 The Author(s).
URI
http://hdl.handle.net/20.500.11750/12695
DOI
10.1186/s13059-020-02092-2
Publisher
BioMed Central Ltd
Related Researcher
  • Author Kim, Jong Kyoung Laboratory of Single-Cell Genomics
  • Research Interests Single-cell genomics, Bioinformatics, Machine Learning
Files:
Collection:
Department of New BiologyETC1. Journal Articles
Department of New BiologyLaboratory of Single-Cell Genomics1. Journal Articles


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