Browsing by Author "Hasheminasabgorji, Elham"

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    Epigenetic Investigation of PF(A) Ependymoma
    (2024-09-13) Hasheminasabgorji, Elham; Gallo, Marco; Nikolic, Ana; Bahlis, Nizar; Chan, Jennifer
    Posterior Fossa type A (PFA) ependymoma in infants presents therapeutic challenges with a 60% survival rate and significant treatment-associated neurocognitive sequalae. Our research revealed a distinctive 3D genomic architecture — Type B Ultra-Long Interactions in PFA (TULIPs) - universally present in PFA samples and occurring at recurrent regions of the genome. Here, we investigate the molecular origins of TULIPs in PFA ependymoma. We hypothesized that EZHIP expression may underlie TULIP formation, given its widespread expression in virtually all PFAs. To test this hypothesis, EZHIP was expressed in human neural progenitor cell (hNPC) cultures, and we validated the models using immunofluorescence and western blot assays. Our results demonstrated the nuclear localization of EZHIP and its association with chromatin. Moreover, the expression of EZHIP induced profound alterations in the conformation and localization of heterochromatin in the cells, consistent with the induction of TULIPs. Additionally, functional EdU incorporation assays provided evidence that the expression of EZHIP positively influences cell proliferation. Based on our immunofluorescence results, TULIPs appear as large H3K9me3-rich foci in the nucleus of cells. In various cell types, regions of heterochromatin marked by H3K9me3 are typically associated with HP1 proteins. Considering that HP1 proteins are involved in maintaining the liquid-liquid phase separation (LLPS) state of H3K9me3, we assessed whether TULIPs were in fact condensates. hNPCs expressing EZHIP were treated with 1,6-hexanediol, a compound widely used to disrupt liquid condensates. Our results indicated that 1,6-hexanediol treatment caused disruption of the H3K9me3 configuration, suggesting that TULIPs are in fact in LLPS states. In conclusion, our study provides valuable insights into the molecular origins of TULIPs in PFA ependymoma, elucidating the role of EZHIP expression and its impact on chromatin conformation and cell proliferation. While our data suggest that TULIPs may exist in an LLPS state, further investigation is required to confirm this. These findings enrich our understanding of the molecular landscape of PFA ependymomas and offer potential therapeutic targets.