
==== Front
Res Sq
ResearchSquare
Research Square
2693-5015
American Journal Experts

10.21203/rs.3.rs-4390765/v2
10.21203/rs.3.rs-4390765
preprint
2
Article
The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells
Yang Jun https://orcid.org/0000-0002-0770-9659

Fang Jie
Singh Shivendra
Wells Brennan
Wu Qiong https://orcid.org/0000-0002-6063-0800

Jin Hongjian
Janke Laura
Wan Shibiao https://orcid.org/0000-0003-0661-2684

Steele Jacob https://orcid.org/0000-0001-9924-2226

Connelly Jon https://orcid.org/0000-0002-5564-1775

Murphy Andrew https://orcid.org/0000-0001-6747-0355

Wang Ruoning https://orcid.org/0000-0001-9798-8032

Davidoff Andrew https://orcid.org/0000-0001-7900-2794

Ashcroft Margaret https://orcid.org/0000-0002-0066-3707

Pruett-Miller Shondra https://orcid.org/0000-0002-3793-585X

13 9 2024
rs.3.rs-4390765https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
https://www.researchsquare.com/article/rs-4390765/v2
nihpp-rs4390765v2.pdf
Abstract

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 a 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 TGFb-SMAD 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.
==== Body
pmc
