Fang Jie, Singh Shivendra, Wells Brennan, Wu Qiong, Jin Hongjian, Janke Laura J, Wan Shibiao, Steele Jacob A, Connelly Jon P, Murphy Andrew J, Wang Ruoning, Davidoff Andrew, Ashcroft Margaret, Pruett-Miller Shondra M, Yang Jun
Department of Surgery, St Jude Children's Research Hospital, Memphis, United States.
Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, United States.
Elife. 2025 May 6;14:RP101299. doi: 10.7554/eLife.101299.
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 (, , and ) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of due to a reduction of expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic, and organogenesis signaling dependencies under different cellular settings.
3D细胞特异性表观遗传和转录组重编程对于器官发生和肿瘤发生至关重要。在此，我们剖析了MYC驱动的小鼠肝癌模型在2D（常氧与慢性缺氧）与3D（常氧）培养条件下不同的细胞适应性。我们鉴定出600多个共享的必需基因以及其他特定背景的适应性基因和途径。在常氧与1%氧气或3D培养条件下，VHL - HIF1途径的敲除导致不相容的适应性缺陷。此外，线粒体呼吸电子传递链复合物中每个复合物的缺失都有不同的适应性结果。值得注意的是，包括TGFβ - SMAD在内的多细胞器官发生信号通路在3D培养中上调，在3D中特异性限制不受控制的细胞增殖，而表观遗传修饰因子（、、和）的失活在2D与3D中有相反的结果。我们进一步鉴定出由于3D特异性表观遗传重编程导致表达降低而与部分缺失相关的3D依赖性合成致死性。我们的研究突出了不同细胞环境下独特的表观遗传、代谢和器官发生信号依赖性。
