Condensates in Ependymoma

PROJECT SUMMARY - PROJECT 3 Ependymoma (EPN) is the third most common pediatric brain tumor. Treatment for EPN has remained unchanged in the last 30 years, consisting of surgery and radiation, with no targeted therapies available to patients. EPNs that arise in the cortex are often driven by a single genetic event involving a fusion of the zinc finger translocation associated (ZFTA) gene and an additional partner, commonly a transcription factor or co- activator protein. ZFTA fusion oncoproteins (FOs) are potent drivers of cancer, and their expression in neural stem cells alone, leads to transformation and tumor development. ZFTA FOs bind DNA at specific sites in the genome to activate oncogenic transcription. However, the mechanisms that govern the recruitment of transcriptional activation and chromatin remodeling proteins following ZFTA FO binding is poorly defined. To understand how ZFTA FOs function to recruit a cascade of transcriptional regulatory proteins to oncogenic loci, we collaborated with the KriwackiLab to apply the FO-Puncta machine learning (ML) model to dissect potentially significant IDRs found within ZFTA FOs. Through ML directed mutagenesis we interrogated the most common ZFTA FO (ZFTA-RELA) and found that a specific IDR was necessary for i) Condensate formation, ii) Chromatin Binding, iii) Gene Activation, and iv) Tumor initiation. We therefore hypothesize that ZFTA FO variants acquire the capacity to form biomolecular condensates that are required for oncogenic transcription and tumor initiation. Studying the mechanisms and compositions of ZFTA FO condensates may provide critical insights into the pathogenesis of EPN and opportunities for therapeutic development. To this end, Project 3, seeks to: 1) To understand how ZFTA FO IDRs drive condensate formation and gene transcription, 2) To understand the impact of ZFTA FO condensates on tumor initiation, and 3) To test how pharmacologic disruption of ZFTA condensates impacts oncogene transcription.