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Title: Genetic dissection of EGFRvIII brain and spinal mouse gliomas through whole-exome sequencing and in vivo piggyBac mutagenesis forward genetic screening
Author: Noorani, Imran
ISNI:       0000 0004 7968 4889
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2019
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Glioma is the commonest intrinsic brain tumor, and its high-grade form has a devastating prognosis. These tumors also arise in the spinal cord, carrying significant morbidity in children; however the genetics of these spinal gliomas is poorly understood. EGFRvIII is a common driver mutation in brain gliomas; it is unclear when this is acquired during glioma evolution and what its cooperative genetic drivers are. Here, we show that EGFRvIII initiates gliomagenesis in vivo; EGFRvIII leads to glioma precursors in the subventricular zone and brain surface, and later glioma formation in the brain and spinal cord. The long latency for tumor formation implies the need for additional mutations to drive gliomagenesis. In these tumors, we detected further genetic alterations including amplification of EGFRvIII, mutations of Trp53 and Tead2, and Cdkn2a deletion, through whole-exome sequencing. To shed further light on EGFR-cooperative genes for glioma progression, we conducted a genome-wide piggyBac transposon mutagenesis screen in vivo, which identified known glioma drivers (including Cdkn2a, Pten and Nf1) and novel putative partners, including genes that regulate neuronal differentiation such as Sox6 and Tcf12, and a novel regulator of the Ras pathway Spred1. RNA-sequencing confirmed the presence of fusion transcripts (transposon mediated effects) for these genes. We demonstrate the clinical relevance of these cooperative genes through comparison with large human glioma databases, demonstrating recurrent genetic alterations of these genes are in patient tumors implicating them as putative drivers, and we highlight that expression levels of Sox6 and Tcf12 correlate with patient prognosis. We show that there are shared and distinct mutated genes in brain and spinal gliomas. Although Pten is a well-known tumor suppressor for brain gliomas, it was not previously known whether Pten drives spinal gliomagenesis. Given recurrent transposon insertions in Pten were found in both brain and spinal gliomas, we generated conditional mice with EGFRvIII and Pten loss, demonstrating Pten accelerates spinal glioma formation. Our work elucidates the genetic evolutionary processes behind EGFRvIII-driven gliomas, provides a detailed genomic comparison between brain and spinal gliomas, and provides functional genomic datasets to help decipher complex human glioma genomes.
Supervisor: Bradley, Allan Sponsor: Wellcome Trust
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
Keywords: Gliomas ; genetic drivers ; functional genomics ; cancer mouse models