Coessential Genetic Networks Reveal the Organization and Constituents of a Dynamic Cellular Stress Response

Abstract

The interrelated programs essential for cellular fitness in the face of stress are critical to understanding tumorigenesis, neurodegeneration, and aging. However, modelling the combinatorial landscape of stresses experienced by diseased cells is challenging, leaving functional relationships within the global stress response network incompletely understood. Here, we leverage genome-scale fitness screening data from 625 cancer cell lines, each representing a unique biological context, to build a network of "coessential" gene relationships centered around master regulators of the response to proteotoxic, oxidative, hypoxic, and genotoxic stress. This approach organizes the stress response into functional modules, identifies genes connecting distinct modules, and reveals mechanisms underlying cellular dependence on individual modules. As an example of the power of this approach, we discover that the previously unannotated HAPSTR (C16orf72) promotes resilience to diverse stressors as a stress-inducible regulator of the E3 ligase HUWE1. Altogether, we present a broadly applicable framework and interactive tool (http://fireworks.mendillolab.org/) to interrogate biological networks using unbiased genetic screens.

Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition

“…A growing list of HUWE1 substrates has since been reported ( Kao et al, 2018 ), including the stress-responsive regulator of mTORC1 signaling, DDIT4 ( Brugarolas et al, 2004 ; Thompson et al, 2014 ), and many DNA damage response factors, such as the BRCA1 tumor suppressor, TopBP1, Cdc6, and CHEK1 ( Cassidy et al, 2020 ; Hall et al, 2007 ; Herold et al, 2008 ; Wang et al, 2014 ). Loss of HUWE1 sensitizes cells not only to DNA damage but also to a variety of other stressors, including both oxidative and hypoxic stress ( Amici et al, 2019 ; Bosshard et al, 2017 ; Clements et al, 2019 ; Kao et al, 2018 ; Olivieri et al, 2020 ). In addition, HUWE1 has been shown to mediate the destruction of unassembled constituents of multi-protein complexes and free histones ( Liu et al, 2005 ; Singh et al, 2009a , 2009b ; Xu et al, 2016 ), contributing to protein quality control ( Sung et al, 2016 ; Xu et al, 2016 ) and cell cycle checkpoint decisions.…”

Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

“…In addition, analysis of coessentiality across 789 cancer cell lines from the DepMap project showed a striking association between C16orf72 and several positive and negative p53 regulators ( Fig. 4e and f) 51, 53 . Together, these data identified C16orf72 as a candidate negative regulator of p53 stability.…”

Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors

“…A growing list of HUWE1 substrates has since been reported 9 , including the stress-responsive regulator of mTORC1 signaling, DDIT4 10,11 , and many DNA damage response factors, such as the BRCA1 tumor suppressor, TopBP1, Cdc6 and CHEK1 [12][13][14][15] . Loss of HUWE1 sensitizes cells not only to DNA damage, but also to a variety of other stressors, including both oxidative and hypoxic stress 9,[16][17][18][19] . In addition, HUWE1 has been shown to mediate the destruction of unassembled constituents of multi-protein complexes, contributing to protein quality control 20,21 .…”