Transcriptional activation of RCOR2 as a novel oncogenic mechanism in supratentorial ependymoma

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PROJECT SUMMARY Brain and other tumors of the central-nervous system (CNS) are the most common cancers in children aged 0-14 years in the USA. Ependymoma (EPN) is the third most common pediatric brain tumor and a leading cause of death in childhood cancer patients. The two most common and most aggressive molecular subgroups of ependymoma are the supratentorial ZFTA/C11orf95-fusion associated group (ST-ZFTA-EPN, formerly ST-RELA-EPN) and the posterior fossa ependymoma group A (PF-A-EPN). Although the molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. The overall objective of this proposal is to identify molecular mechanisms underlying aberrant expression of genes that are essential for tumorigenesis and contribute to the poor survival of ST-ZFTA-EPN patients. To approach this objective, we have analyzed the 3D conformation of primary ST-ZFTA-EPN tumors and cell lines using genome-wide chromosome conformation capture (Hi-C). As a result, we observe the formation of new topologically associating domains (‘neo-TADs’) induced by structural variants (SVs) in all ST-ZFTA-EPN tumors, placing the REST Corepressor 2 (RCOR2) gene into a new regulatory environment. By evaluating Affymetrix gene expression array data across ependymoma groups, we found that RCOR2 transcription is significantly upregulated in ST-ZFTA-EPN relative to other ependymoma groups. Through inhibition experiments, we validated that RCOR2 is highly essential for the survival of a patient-derived ST-ZFTA-EPN cell line in a disease subtype-specific manner. Based on these preliminary results, we now hypothesize that transcriptional activation of RCOR2 is induced by structural variants and the formation of neo-TADs, which contributes to tumorigenesis in ST-ZFTA-EPN patients. The central hypothesis will be tested by pursuing to answer two specific aims: First, we aim to functionally validate transcriptional activation of RCOR2 by structural variants and the formation of neo-TADs (Specific Aim 1). Second, we aim to dissect the role of RCOR2 in tumorigenesis of supratentorial ZFTA- RELA fusion associated ependymomas (Specific Aim 2). The rationale for this project is that experiments studying the function of RCOR2 in patient-derived models of ST-ZFTA-EPN tumors are likely to provide a strong scientific framework in which basic mechanisms of ependymoma tumorigenesis and new therapeutic opportunities can be identified. The research proposed in this application is innovative, in the applicant’s opinion, because it interrogates a novel molecular mechanism of transcriptional RCOR2 activation in recently derived faithful models of ST-ZFTA-EPN. The proposed research is significant, because it is expected to provide new therapeutic opportunities for a pediatric brain tumor type that is a leading cause of death in childhood cancer patients. Ultimately, our studies have the potential to functionally validate RCOR2 and its associated protein complexes as drivers of ST-ZFTA-EPN tumors and as a novel therapeutic vulnerability in this devastating disease.