This project addresses the fundamental question of how cells adjust their gene expression program in response to oxidative stress (OS) in order to ensure survival. OS, inflicted upon cells either as an intrinsic cost of aerobic metabolism or by extraneous conditions, is intimately linked to a variety of ageing-related diseases, including neurodegenerative disorders, inflammatory conditions, cancer, and the vascular complications of diabetes. OS is known to trigger a transcriptional program primarily geared toward recovery, but triggering cell death if the damage is irreparable. Whereas this program is relatively well characterized at the level of mRNA abundance, almost nothing is known about the coordination with posttranscriptional layers of gene expression control. This application explores the overarching hypothesis that gene expression in response to OS is shaped by an integrated multi-layered program that precisely coordinates transcriptional and posttranscriptional mechanisms to maximize survival.
The aim i s to describe these mechanisms quantitatively and validating them experimentally both by acquiring global gene expression datasets and by formalizing the connections in mathematical terms. Specifically, a novel model of integrated control is addressed that was inspired by preliminary studies which highlighted the limitations of predicting protein changes from changes in mRNA levels. Mathematical simulations suggested critical roles for control at the levels of mRNA and protein stability during stress that lead to te following propositions: a) Increased synthesis of stress-induced proteins coincides with increased oxidative damage and hence increased proteolytic clearance as a quality control mechanism. b) OS-triggered rapid translational shutdown leads to downregulation of OS-suppressed mRNAs but not proteins in order to liberate ribosome capacity for the efficient translation of OS-induced mRNAs. Within the realm of the proposed project, these predictions will be put to scrutiny by acquiring unique system-wide datasets that will feed into an iterative process of mathematical modeling and experimental validation to arrive at a comprehensive framework of stress-regulated gene expression. The studies also address the general applicability of the OS models for gene expression in response to other forms of environmental stress and to mammalian cells.

Public Health Relevance

Oxidative stress is thought to be at the root of many highly prevalent chronic diseases, including neurodegenerative disorders, inflammatory diseases, cancer, and diabetes. The studies proposed here will examine fundamental mechanisms of oxidative stress response that may lead to novel targets for drugs aimed at alleviating these diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM105802-04
Application #
9207017
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Reddy, Michael K
Project Start
2014-01-01
Project End
2017-12-31
Budget Start
2017-01-01
Budget End
2017-12-31
Support Year
4
Fiscal Year
2017
Total Cost
$333,450
Indirect Cost
$162,450
Name
Sanford Burnham Prebys Medical Discovery Institute
Department
Type
Research Institutes
DUNS #
020520466
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Sanchez, Marisa; Xia, Zebin; Rico-Bautista, Elizabeth et al. (2018) Oxidized analogs of Di(1H-indol-3-yl)methyl-4-substituted benzenes are NR4A1-dependent UPR inducers with potent and safe anti-cancer activity. Oncotarget 9:25057-25074
Dubiel, Wolfgang; Dubiel, Dawadschargal; Wolf, Dieter A et al. (2018) Cullin 3-Based Ubiquitin Ligases as Master Regulators of Mammalian Cell Differentiation. Trends Biochem Sci 43:95-107
Attali, Ilan; Tobelaim, William Sam; Persaud, Avinash et al. (2017) Ubiquitylation-dependent oligomerization regulates activity of Nedd4 ligases. EMBO J 36:425-440
Straube, Ronny; Shah, Meera; Flockerzi, Dietrich et al. (2017) Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire. PLoS Comput Biol 13:e1005869
Wolf, Dieter A; Bähler, Jürg; Wise, Jo Ann (2017) Schizosaccharomyces pombe Polysome Profile Analysis and RNA Purification. Cold Spring Harb Protoc 2017:pdb.prot091637
Shah, Meera; Su, Dan; Scheliga, Judith S et al. (2016) A Transcript-Specific eIF3 Complex Mediates Global Translational Control of Energy Metabolism. Cell Rep 16:1891-902
Fan, Jun-Bao; Arimoto, Kei-ichiro; Motamedchaboki, Khatereh et al. (2015) Identification and characterization of a novel ISG15-ubiquitin mixed chain and its role in regulating protein homeostasis. Sci Rep 5:12704
Wolf, Dieter A (2014) Is reliance on mitochondrial respiration a ""chink in the armor"" of therapy-resistant cancer? Cancer Cell 26:788-795