Genetic Screen for Cell Fitness in High or Low Oxygen Highlights Mitochondrial and Lipid Metabolism

• Published in: Cell Vol. 181; no. 3; pp. 716 - 727.e11
• Main Authors: Jain, Isha H., Calvo, Sarah E., Markhard, Andrew L., Skinner, Owen S., To, Tsz-Leung, Ast, Tslil, Mootha, Vamsi K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 30-04-2020; Elsevier
• Subjects: Cell Hypoxia; CoQ biosynthesis; FASII; Genetic Testing - methods; Genome-Wide Association Study - methods; HEK293 Cells; Humans; hypoxia; Hypoxia - metabolism; iron-sulfur clusters; K562 Cells; Lipid Metabolism - genetics; Lipid Metabolism - physiology; Lipids - genetics; Lipids - physiology; membrane fluidity; Mitochondria - genetics; Mitochondria - metabolism; MPC; Oxygen - metabolism; plasmalogens; pyruvate dehydrogenase; Reactive Oxygen Species - metabolism; Signal Transduction - physiology; TMEM189; Transcriptome - genetics; type II fatty acid synthesis; pyruvate dehydrogenase; hypoxia; MPC; FASII; plasmalogens; TMEM189; type II fatty acid synthesis; iron-sulfur clusters; CoQ biosynthesis; membrane fluidity
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2020.03.029

Human cells are able to sense and adapt to variations in oxygen levels. Historically, much research in this field has focused on hypoxia-inducible factor (HIF) signaling and reactive oxygen species (ROS). Here, we perform genome-wide CRISPR growth screens at 21%, 5%, and 1% oxygen to systematically identify gene knockouts with relative fitness defects in high oxygen (213 genes) or low oxygen (109 genes), most without known connection to HIF or ROS. Knockouts of many mitochondrial pathways thought to be essential, including complex I and enzymes in Fe-S biosynthesis, grow relatively well at low oxygen and thus are buffered by hypoxia. In contrast, in certain cell types, knockout of lipid biosynthetic and peroxisomal genes causes fitness defects only in low oxygen. Our resource nominates genetic diseases whose severity may be modulated by oxygen and links hundreds of genes to oxygen homeostasis.
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•CRISPR screens at 21%, 5%, and 1% O2 highlight 322 genes, most unconnected to HIF•Low O2 buffers loss of mitochondrial and Fe-S biosynthetic pathways•Low O2 exacerbates loss of pathways in lipid and peroxisomal metabolism•Screen nominates genetic diseases that may benefit from O2-modulation
Cells in tissues experience different levels of oxygen, and investigating how individual genes contribute to fitness in response to changing oxygen tension uncovers key cellular response pathways and points to examples where modulation of oxygen levels may positively impact genetic disease.