Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression
Background: MYCN amplification and high expression is associated with pediatric malignancies including neuroblastoma and alveolar rhabdomyosarcoma. MYCN transcription in alveolar rhabdomyosarcomas is driven by a feedback loop with the PAX3::FOXO1 fusion protein. However, the role of MYCN is not well...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-06-01
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| Series: | EJC Paediatric Oncology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2772610X25000170 |
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| author | Zoë S. Walters Daniel Leongamornlert Barbara Villarejo-Balcells Carmen Tse Reuben Pengelly Ian Titley Janet Shipley |
| author_facet | Zoë S. Walters Daniel Leongamornlert Barbara Villarejo-Balcells Carmen Tse Reuben Pengelly Ian Titley Janet Shipley |
| author_sort | Zoë S. Walters |
| collection | DOAJ |
| description | Background: MYCN amplification and high expression is associated with pediatric malignancies including neuroblastoma and alveolar rhabdomyosarcoma. MYCN transcription in alveolar rhabdomyosarcomas is driven by a feedback loop with the PAX3::FOXO1 fusion protein. However, the role of MYCN is not well-defined. Methods: Chromatin ImmunoPrecipitation (ChIP)-sequencing of alveolar rhabdomyosarcoma cell lines was used to identify genome-wide MYCN binding sites. Ontology analyses of genes adjacent to MYCN binding sites corresponding to expression changes after siRNA reduction was performed and confirmed by ChIP-qPCR. Cells from each phase of the cell cycle were isolated by Fluorescence Activated Cell Sorting for assessing protein expression by Western blotting. Results: Genes encoding transcription factors adjacent to MYCN binding sites and genes with binding sites proximal to their promoters were strongly associated with RNA synthesis and cell cycle pathways, respectively. MYCN binding sites in regions that positively correlated with gene expression changes were linked to cell cycle regulation, consistent with phenotypic absence of cell cycle checkpoint control. Cell cycle regulated genes CDK4 and KDM4B were validated as MYCN-regulated and, in-keeping with unchecked cell cycle progression, expressed throughout the cell cycle, coincident with MYCN. Conclusions: MYCN binding sites associated with gene expression changes defined the contribution of MYCN to the transcriptional control of key pathways/molecular processes in the development and progression of rhabdomyosarcomas. MYCN aberrantly regulated CDK4 and KDM4B expression throughout the cell cycle in PAX3::FOXO1 positive rhabdomyosarcoma. The regulatory network defined supports MYCN, CDK4 and KDM4B as therapeutic targets in the treatment of rhabdomyosarcoma patients. |
| format | Article |
| id | doaj-art-a98f136f0aaa44b5bffdf3f2c634f767 |
| institution | OA Journals |
| issn | 2772-610X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EJC Paediatric Oncology |
| spelling | doaj-art-a98f136f0aaa44b5bffdf3f2c634f7672025-08-20T02:36:58ZengElsevierEJC Paediatric Oncology2772-610X2025-06-01510023010.1016/j.ejcped.2025.100230Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progressionZoë S. Walters0Daniel Leongamornlert1Barbara Villarejo-Balcells2Carmen Tse3Reuben Pengelly4Ian Titley5Janet Shipley6Division of Molecular Pathology, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; Innovation for Translation Research Group (ITRG), Cancer Sciences, Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UKOncogenetics, The Institute of Cancer Research, Sutton, London SM2 5NG, UKDivision of Molecular Pathology, The Institute of Cancer Research, Sutton, London SM2 5NG, UKInnovation for Translation Research Group (ITRG), Cancer Sciences, Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UKHuman Development and Health, Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UKResearch Operations, The Institute of Cancer Research, Sutton, London SM2 5NG, UKDivision of Molecular Pathology, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; Correspondence to: Sarcoma Molecular Pathology, Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.Background: MYCN amplification and high expression is associated with pediatric malignancies including neuroblastoma and alveolar rhabdomyosarcoma. MYCN transcription in alveolar rhabdomyosarcomas is driven by a feedback loop with the PAX3::FOXO1 fusion protein. However, the role of MYCN is not well-defined. Methods: Chromatin ImmunoPrecipitation (ChIP)-sequencing of alveolar rhabdomyosarcoma cell lines was used to identify genome-wide MYCN binding sites. Ontology analyses of genes adjacent to MYCN binding sites corresponding to expression changes after siRNA reduction was performed and confirmed by ChIP-qPCR. Cells from each phase of the cell cycle were isolated by Fluorescence Activated Cell Sorting for assessing protein expression by Western blotting. Results: Genes encoding transcription factors adjacent to MYCN binding sites and genes with binding sites proximal to their promoters were strongly associated with RNA synthesis and cell cycle pathways, respectively. MYCN binding sites in regions that positively correlated with gene expression changes were linked to cell cycle regulation, consistent with phenotypic absence of cell cycle checkpoint control. Cell cycle regulated genes CDK4 and KDM4B were validated as MYCN-regulated and, in-keeping with unchecked cell cycle progression, expressed throughout the cell cycle, coincident with MYCN. Conclusions: MYCN binding sites associated with gene expression changes defined the contribution of MYCN to the transcriptional control of key pathways/molecular processes in the development and progression of rhabdomyosarcomas. MYCN aberrantly regulated CDK4 and KDM4B expression throughout the cell cycle in PAX3::FOXO1 positive rhabdomyosarcoma. The regulatory network defined supports MYCN, CDK4 and KDM4B as therapeutic targets in the treatment of rhabdomyosarcoma patients.http://www.sciencedirect.com/science/article/pii/S2772610X25000170MYCNChIP-sequencingCell cycleRhabdomyosarcomaCDK6KDM4B |
| spellingShingle | Zoë S. Walters Daniel Leongamornlert Barbara Villarejo-Balcells Carmen Tse Reuben Pengelly Ian Titley Janet Shipley Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression EJC Paediatric Oncology MYCN ChIP-sequencing Cell cycle Rhabdomyosarcoma CDK6 KDM4B |
| title | Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression |
| title_full | Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression |
| title_fullStr | Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression |
| title_full_unstemmed | Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression |
| title_short | Transcriptional regulation of genes by MYCN in PAX3::FOXO1-positive rhabdomyosarcomas and their roles in cell cycle progression |
| title_sort | transcriptional regulation of genes by mycn in pax3 foxo1 positive rhabdomyosarcomas and their roles in cell cycle progression |
| topic | MYCN ChIP-sequencing Cell cycle Rhabdomyosarcoma CDK6 KDM4B |
| url | http://www.sciencedirect.com/science/article/pii/S2772610X25000170 |
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