{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/159087"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/159087","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Identifying the Role of Transcription Factor RFX3 in 9PDeletion Syndrome","abstract":"9p deletion (9p-) syndrome is primarily characterized by intellectual disability, developmental delays, and autism. This project investigated how much of the neuronal phenotypes of 9p- syndrome could be attributed to RFX3, a transcription factor and autism risk gene. Bulk RNA-seq data of iPSC-derived neurons from patients with 9p- syndrome and CRISPRengineered cell lines was analyzed using Principal Component Analysis, Differential Gene Expression analysis, and Functional Enrichment analysis. The findings indicate that RFX3 plays a significant role but is not the sole driver of the neuronal phenotypes. SMARCA2, a gene linked to intellectual disability and part of the SWI/SNF complex, was identified as a direct target of RFX3 in the commonly deleted region of chromosome 9p. Notably, the combined deletion of RFX3 and SMARCA2 led to greater dysregulation of SMARCA2 expression and SWI/SNF complex components than the deletion of either gene alone. These findings highlight the potential synergistic effects of RFX3 and SMARCA2 in 9p- syndrome and suggest their combined disruption may underlie the neuronal phenotypes observed.","abstract_html":"9p deletion (9p-) syndrome is primarily characterized by intellectual disability, developmental delays, and autism. This project investigated how much of the neuronal phenotypes of 9p- syndrome could be attributed to RFX3, a transcription factor and autism risk gene. Bulk RNA-seq data of iPSC-derived neurons from patients with 9p- syndrome and CRISPRengineered cell lines was analyzed using Principal Component Analysis, Differential Gene Expression analysis, and Functional Enrichment analysis. The findings indicate that RFX3 plays a significant role but is not the sole driver of the neuronal phenotypes. SMARCA2, a gene linked to intellectual disability and part of the SWI/SNF complex, was identified as a direct target of RFX3 in the commonly deleted region of chromosome 9p. Notably, the combined deletion of RFX3 and SMARCA2 led to greater dysregulation of SMARCA2 expression and SWI/SNF complex components than the deletion of either gene alone. These findings highlight the potential synergistic effects of RFX3 and SMARCA2 in 9p- syndrome and suggest their combined disruption may underlie the neuronal phenotypes observed.","abstract_has_math":false,"creators":["Edwards, Lilly"],"institution":"Massachusetts Institute of Technology","degree_name":"Master","degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science","school":null,"contributors":[],"advisors":["Yu, Timothy","Lee, Eunjung Alice","Kellis, Manolis"],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-02","date_published":"2025-02","updated_at":"2026-07-22T22:21:22Z","subjects":[],"languages":[],"rights":["In Copyright - Educational Use Permitted","Copyright retained by author(s)"],"rights_urls":["https://rightsstatements.org/page/InC-EDU/1.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/1721.1/159087","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Yu, Timothy","Lee, Eunjung Alice","Kellis, Manolis"]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. 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This project investigated how much of the neuronal phenotypes of 9p- syndrome could be attributed to RFX3, a transcription factor and autism risk gene. Bulk RNA-seq data of iPSC-derived neurons from patients with 9p- syndrome and CRISPRengineered cell lines was analyzed using Principal Component Analysis, Differential Gene Expression analysis, and Functional Enrichment analysis. The findings indicate that RFX3 plays a significant role but is not the sole driver of the neuronal phenotypes. SMARCA2, a gene linked to intellectual disability and part of the SWI/SNF complex, was identified as a direct target of RFX3 in the commonly deleted region of chromosome 9p. Notably, the combined deletion of RFX3 and SMARCA2 led to greater dysregulation of SMARCA2 expression and SWI/SNF complex components than the deletion of either gene alone. These findings highlight the potential synergistic effects of RFX3 and SMARCA2 in 9p- syndrome and suggest their combined disruption may underlie the neuronal phenotypes observed."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["M.Eng."]},{"key":"dc:title","label":"Title","values":["Identifying the Role of Transcription Factor RFX3 in 9PDeletion Syndrome"]}]}],"canonical_facts":{"dc:contributor.advisor":["Yu, Timothy","Lee, Eunjung Alice","Kellis, Manolis"],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science"],"dc:creator":["Edwards, Lilly"],"dc:date.accessioned":["2025-04-14T14:04:38Z"],"dc:date.available":["2025-04-14T14:04:38Z"],"dc:date.issued":["2025-02"],"dc:description.abstract":["9p deletion (9p-) syndrome is primarily characterized by intellectual disability, developmental delays, and autism. This project investigated how much of the neuronal phenotypes of 9p- syndrome could be attributed to RFX3, a transcription factor and autism risk gene. Bulk RNA-seq data of iPSC-derived neurons from patients with 9p- syndrome and CRISPRengineered cell lines was analyzed using Principal Component Analysis, Differential Gene Expression analysis, and Functional Enrichment analysis. The findings indicate that RFX3 plays a significant role but is not the sole driver of the neuronal phenotypes. SMARCA2, a gene linked to intellectual disability and part of the SWI/SNF complex, was identified as a direct target of RFX3 in the commonly deleted region of chromosome 9p. Notably, the combined deletion of RFX3 and SMARCA2 led to greater dysregulation of SMARCA2 expression and SWI/SNF complex components than the deletion of either gene alone. These findings highlight the potential synergistic effects of RFX3 and SMARCA2 in 9p- syndrome and suggest their combined disruption may underlie the neuronal phenotypes observed."],"dc:description.degree":["M.Eng."],"dc:identifier.uri":["https://hdl.handle.net/1721.1/159087"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["In Copyright - Educational Use Permitted","Copyright retained by author(s)"],"dc:rights.uri":["https://rightsstatements.org/page/InC-EDU/1.0/"],"dc:title":["Identifying the Role of Transcription Factor RFX3 in 9PDeletion Syndrome"],"dc:type":["Thesis"],"thesis:degree_name":["Master","Master of Engineering in Computer Science and Molecular Biology"]},"updated_at":"2026-07-22T22:21:22Z"}