Epigenetic Investigation of PF(A) Ependymoma

Hasheminasabgorji, Elham

Epigenetic Investigation of PF(A) Ependymoma

dc.contributor.advisor	Gallo, Marco
dc.contributor.advisor	Nikolic, Ana
dc.contributor.author	Hasheminasabgorji, Elham
dc.contributor.committeemember	Bahlis, Nizar
dc.contributor.committeemember	Chan, Jennifer
dc.date	2024-11
dc.date.accessioned	2024-09-16T17:47:22Z
dc.date.available	2024-09-16T17:47:22Z
dc.date.issued	2024-09-13
dc.description.abstract	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.
dc.identifier.citation	Hasheminasabgorji, E. (2024). Epigenetic investigation of PF(A) ependymoma (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.
dc.identifier.uri	https://hdl.handle.net/1880/119731
dc.language.iso	en
dc.publisher.faculty	Graduate Studies
dc.publisher.institution	University of Calgary
dc.rights	University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subject.classification	Biology--Cell
dc.subject.classification	Biology--Molecular
dc.subject.classification	Biogeochemistry
dc.title	Epigenetic Investigation of PF(A) Ependymoma
dc.type	master thesis
thesis.degree.discipline	Medicine – Biochemistry and Molecular Biology
thesis.degree.grantor	University of Calgary
thesis.degree.name	Master of Science (MSc)
ucalgary.thesis.accesssetbystudent	I do not require a thesis withhold – my thesis will have open access and can be viewed and downloaded publicly as soon as possible.