Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development

ZFTA-RELA (ZR) is the most recurrent genetic alteration seen in pediatric supratentorial ependymoma (EPN) and is sufficient to initiate tumors in mice. Despite the oncogenic potential of ZR, it is observed nearly exclusively in childhood EPN, with tumors located distinctly in the supratentorial region of the central nervous system (CNS). We hypothesized that specific chromatin modules accessible during brain development would render distinct cell lineage programs at direct risk of transformation by ZR. To this end, we performed combined single nucleus ATAC and RNA (snMultiome) sequencing of the developing mouse forebrain, as compared to ZR-driven mouse and human EPN. We demonstrate that specific developmental lineage programs present in transient progenitor cells and regulated by PLAG/L family transcription factors (TF) are at risk of neoplastic transformation. Binding of this chromatin network by ZR or other PLAG/L family motif targeting fusion oncoproteins lead to persistent chromatin accessibility at oncogenic loci and oncogene expression. Cross-species analysis of mouse and human ZR EPN reveals significant cell type heterogeneity mirroring incomplete neurogenic and gliogenic differentiation, with a small percentage of cycling progenitor-like or radial glial-like cells that establish a putative tumor cell hierarchy. In vivo lineage tracing studies reveal neoplastic clones that aggressively dominate tumor growth and establish the entire EPN cellular hierarchy. These findings unravel developmental epigenomic states critical for fusion oncoprotein-driven transformation and elucidate how these states continue to shape tumor progression.