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Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis.
Zhao, Dongxin; Badur, Mehmet G; Luebeck, Jens; Magaña, Jose H; Birmingham, Amanda; Sasik, Roman; Ahn, Christopher S; Ideker, Trey; Metallo, Christian M; Mali, Prashant.
Affiliation
  • Zhao D; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
  • Badur MG; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
  • Luebeck J; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
  • Magaña JH; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
  • Birmingham A; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA.
  • Sasik R; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA.
  • Ahn CS; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
  • Ideker T; Department of Medicine, Division of Genetics, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
  • Metallo CM; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA. Electronic address: cmetallo@ucsd.edu.
  • Mali P; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. Electronic address: pmali@ucsd.edu.
Mol Cell ; 69(4): 699-708.e7, 2018 02 15.
Article in En | MEDLINE | ID: mdl-29452643
The metabolic pathways fueling tumor growth have been well characterized, but the specific impact of transforming events on network topology and enzyme essentiality remains poorly understood. To this end, we performed combinatorial CRISPR-Cas9 screens on a set of 51 carbohydrate metabolism genes that represent glycolysis and the pentose phosphate pathway (PPP). This high-throughput methodology enabled systems-level interrogation of metabolic gene dispensability, interactions, and compensation across multiple cell types. The metabolic impact of specific combinatorial knockouts was validated using 13C and 2H isotope tracing, and these assays together revealed key nodes controlling redox homeostasis along the KEAP-NRF2 signaling axis. Specifically, targeting KEAP1 in combination with oxidative PPP genes mitigated the deleterious effects of these knockouts on growth rates. These results demonstrate how our integrated framework, combining genetic, transcriptomic, and flux measurements, can improve elucidation of metabolic network alterations and guide precision targeting of metabolic vulnerabilities based on tumor genetics.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: NF-E2-Related Factor 2 / Metabolic Networks and Pathways / Transcriptome / CRISPR-Cas Systems / Kelch-Like ECH-Associated Protein 1 Limits: Humans Language: En Journal: Mol Cell Journal subject: BIOLOGIA MOLECULAR Year: 2018 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: NF-E2-Related Factor 2 / Metabolic Networks and Pathways / Transcriptome / CRISPR-Cas Systems / Kelch-Like ECH-Associated Protein 1 Limits: Humans Language: En Journal: Mol Cell Journal subject: BIOLOGIA MOLECULAR Year: 2018 Type: Article Affiliation country: United States