The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells
3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here, we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions for an MYC-driven murine liver cancer model. We identify over 600 share...
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eLife Sciences Publications Ltd
2025-05-01
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| Online Access: | https://elifesciences.org/articles/101299 |
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| author | Jie Fang Shivendra Singh Brennan Wells Qiong Wu Hongjian Jin Laura J Janke Shibiao Wan Jacob A Steele Jon P Connelly Andrew J Murphy Ruoning Wang Andrew Davidoff Margaret Ashcroft Shondra M Pruett-Miller Jun Yang |
| author_facet | Jie Fang Shivendra Singh Brennan Wells Qiong Wu Hongjian Jin Laura J Janke Shibiao Wan Jacob A Steele Jon P Connelly Andrew J Murphy Ruoning Wang Andrew Davidoff Margaret Ashcroft Shondra M Pruett-Miller Jun Yang |
| author_sort | Jie Fang |
| collection | DOAJ |
| description | 3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here, we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions for an MYC-driven murine liver cancer model. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFβ-SMAD, which is upregulated in 3D culture, specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3, and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic, and organogenesis signaling dependencies under different cellular settings. |
| format | Article |
| id | doaj-art-85be65549c9e4ad783c27c976fb10fa3 |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-05-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-85be65549c9e4ad783c27c976fb10fa32025-08-20T02:10:39ZengeLife Sciences Publications LtdeLife2050-084X2025-05-011410.7554/eLife.101299The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cellsJie Fang0https://orcid.org/0000-0001-6480-134XShivendra Singh1Brennan Wells2Qiong Wu3https://orcid.org/0000-0002-6063-0800Hongjian Jin4Laura J Janke5Shibiao Wan6Jacob A Steele7https://orcid.org/0000-0001-9924-2226Jon P Connelly8Andrew J Murphy9https://orcid.org/0000-0001-6747-0355Ruoning Wang10https://orcid.org/0000-0001-9798-8032Andrew Davidoff11Margaret Ashcroft12https://orcid.org/0000-0002-0066-3707Shondra M Pruett-Miller13https://orcid.org/0000-0002-3793-585XJun Yang14https://orcid.org/0000-0002-4233-3220Department of Surgery, St Jude Children’s Research Hospital, Memphis, United StatesDepartment of Surgery, St Jude Children’s Research Hospital, Memphis, United StatesDepartment of Surgery, St Jude Children’s Research Hospital, Memphis, United StatesDepartment of Surgery, St Jude Children’s Research Hospital, Memphis, United StatesCenter for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, United StatesDepartment of Pathology and Division of Comparative Pathology, St. Jude Children’s Research Hospital, Memphis, United StatesBioinformatics and Systems Biology Core and Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center, Omaha, United StatesDepartment of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, United StatesDepartment of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, United StatesDepartment of Surgery, St Jude Children’s Research Hospital, Memphis, United StatesCenter for Childhood Cancer Research, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Department of Pediatrics at The Ohio State University, Columbus, United StatesDepartment of Surgery, St Jude Children’s Research Hospital, Memphis, United States; St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, United States; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, Memphis, United StatesDepartment of Medicine, University of Cambridge, Cambridge, United KingdomDepartment of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, United StatesDepartment of Surgery, St Jude Children’s Research Hospital, Memphis, United States; St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, United States; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, Memphis, United States; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, United States3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here, we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions for an MYC-driven murine liver cancer model. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFβ-SMAD, which is upregulated in 3D culture, specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3, and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic, and organogenesis signaling dependencies under different cellular settings.https://elifesciences.org/articles/101299MYCfitnesshypoxiaCRISPR3-dimensionalliver cancer |
| spellingShingle | Jie Fang Shivendra Singh Brennan Wells Qiong Wu Hongjian Jin Laura J Janke Shibiao Wan Jacob A Steele Jon P Connelly Andrew J Murphy Ruoning Wang Andrew Davidoff Margaret Ashcroft Shondra M Pruett-Miller Jun Yang The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells eLife MYC fitness hypoxia CRISPR 3-dimensional liver cancer |
| title | The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells |
| title_full | The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells |
| title_fullStr | The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells |
| title_full_unstemmed | The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells |
| title_short | The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells |
| title_sort | context dependent epigenetic and organogenesis programs determine 3d vs 2d cellular fitness of myc driven murine liver cancer cells |
| topic | MYC fitness hypoxia CRISPR 3-dimensional liver cancer |
| url | https://elifesciences.org/articles/101299 |
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