Development and Application of Model Systems to Study Extrachromosomal DNA Generation in Glioblastoma

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PROJECT SUMMARY/ABSTRACT Glioblastoma (GBM) is the most common primary malignant brain tumor with little improvement in patient survival in past few decades despite aggressive treatment options. Better understanding of the mechanisms underlying GBM is necessary to design more effective therapeutic strategies. Extrachromosomal DNAs (ecDNAs) are a well-known mechanism of oncogene amplification that promotes rapid tumor growth. Although discovered decades ago, recent technological advances have characterized ecDNAs in finer detail and have shown that they are a common occurrence in many cancer types. In a pan-cancer analysis, patients whose tumors had ecDNA amplifications were found to have significantly shorter survival than patients whose tumors had other types of amplifications. A recent study using GBM patient tumor tissues, their derivative cell lines, and orthotopic xenograft mouse models generated from these lines, showed that the majority of oncogene amplifications in these systems are extrachromosomal. Indeed, studies have shown that around 60% of GBM tumors contain ecDNAs, making it the cancer with highest ecDNA prevalence. Mechanisms that enable ecDNA generation at such high rates in GBM are starting to be revealed; however, no model systems are currently available to causally analyze the role of specific genes in their generation. In Aim 1, we will therefore utilize a drug resistance mechanism that allows ecDNA generation to develop clonal lines from primary patient-derived GBM cells to model ecDNA generation. These systems will be isogenic (i.e., without/before and with/after ecDNA generation) and clonal to minimize intercellular heterogeneity in ecDNA levels. Procurement of clones before and after ecDNA generation, and knowledge of clones that are able to generate ecDNAs in this approach, combined with desired manipulations of genes of interest permits assessment of causality of those genes in the generation process. Using these model systems developed, we will test a hypothesis in Aim 2 that DNA repair machinery is necessary for ecDNA generation with specific DNA repair genes governing the process. There is increasing evidence implicating DNA repair in ecDNA generation. Moreover, DNA repair is actively being studied as a target for GBM treatment due to its well-documented role in resistance to standard therapy for GBM via repair of therapy-induced DNA damage. The causal role of key DNA repair genes in ecDNA generation will be analyzed by determining the effects of CRISPRi-induced repression of these genes on ecDNA generation. We expect that the findings from this project will help define the ecDNA generation process and the therapeutic potential of targeting ecDNA in GBM with implications for other cancers with high ecDNA prevalence.