Mechanistic and Functional Genomic Interrogation of Meningioma Radiotherapy Response Genes

PROJECT SUMMARY The World Health Organization (WHO) has historically graded meningiomas according to histological features, and many WHO grade 1 meningiomas can be effectively treated with surgery or radiotherapy, but many WHO grade 2 or grade 3 meningiomas are resistant to treatment and cause significant neurological morbidity and mortality. Approximately 30% of WHO grade 1 meningioma develop recurrences that cannot be predicted from histological features, and some WHO grade 2 or grade 3 meningiomas are unexpectedly well controlled with surgery and radiotherapy. These data indicate that improvements in risk stratification and new therapies for patients with meningiomas are needed, but limited understanding of meningioma biology and the misconception that all meningiomas are benign has encumbered medical and scientific advances for patients with meningiomas. Using multiplatform molecular profiling on 1856 meningiomas from 12 institutions across 3 continents, we discovered a 34-gene expression biomarker that improve risk stratification compared to all other classification systems across all WHO grades. Moreover, our data demonstrate that gene expression profiling predicts which meningiomas will benefit from postoperative radiotherapy (32%). Cooperative group trials, clinical guidelines, and classification systems that incorporate our gene expression biomarker are under development. More broadly, the development of this biomarker provides a framework for understanding how meningiomas grow and respond to therapy, but it is unclear if the 34 genes that comprise this biomarker are drivers or merely markers of meningioma biology. Here we propose mechanistic and functional genomic interrogation of meningioma radiotherapy response genes using traditional mechanistic and function approaches (Aim 1) and a novel technique that links genetic and therapeutic perturbations to genomic phenotypes in single cells (Aim 2) across a unique biobank of meningioma cell lines that represent each meningioma DNA methylation group in humans. Our central hypothesis that the genes comprising our predictive biomarker of meningioma outcomes in humans represent therapeutic vulnerabilities that could enhance radiotherapy responses. Our studies will use genetic loss-of-function and rescue approaches alongside proliferation, clonogenic growth, and apoptosis assays (Aim 1) and simultaneous single-nuclei ATAC, RNA, and CRISPRi perturbation sequencing (snARC- seq) to perform mechanistic and functional genomic interrogation of meningioma radiotherapy response genes. To do so, we have assembled a biobank of 27 patient-derived meningioma cell lines that represent all DNA methylation groups in humans and completed a genome-wide CRISPRi screen to shed light on which genes from our 34-gene expression biomarker underly meningioma growth or response to radiotherapy. Successful completion of this project will determine if the 34 genes comprising our predictive biomarker are drivers of meningioma biology and will elucidate targets for future pharmacological studies in preclinical xenograft models and early phase clinical trials in patients.