CSIG-16. RECONCILING TUMOR HETEROGENEITY IN GLIOBLASTOMA USING A PATHWAY-BASED APPROACH

Abstract

Abstract Despite efforts to gain a deeper understanding of its molecular architecture, glioblastoma (GBM) remains uniformly fatal. While genome-based molecular subtyping has revealed that GBMs may be parsed into several distinct molecular categories, this insight has yielded little progress towards extending patient survival. In particular, the great phenotypic heterogeneity of GBM – both inter and intratumorally – has hindered therapeutic efforts. To this end, we interrogated tumor samples using a pathway-based approach to resolve tumoral heterogeneity. Gene set enrichment analysis (GSEA) was applied to gene expression data and used to provide an overview of each sample that was then compared to others, generating sample clusters based on overall patterns of enrichment. The Cancer Genome Atlas (TCGA) samples were clustered using canonical and oncogenic signatures and in both cases the clustering was distinct from the molecular subtypes previously reported. Using principal component analysis (PCA) and other bioinformatics tools, we extracted gene sets to further characterize the pathways contributing to each of these clusters. We generated gene lists of the top common elements and Ingenuity pathway analysis exposed molecular targets that control critical pathways of each identified cluster. Similar analyses were completed in a gene expression database of patient-derived gliomasphere lines and molecular targets were also obtained. We found E2F1 to be a strong target based on gene lists from both databases. A cluster of gliomasphere lines have high enrichment scores for the gene list predicted to depend on E2F1. In vitro genetic perturbation showed decrease stem cell frequency and lower expression of cell cycle progression genes in cell lines from this cluster exclusively. Other cluster-specific targets are being validated and in vivo studies will follow momentarily. Our studies relate intertumoral heterogeneity to critical cellular pathways dysregulated in GBM, with the ultimate goal of establishing a pipeline for patient- and tumor-specific precision medicine.