Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis

Katherine Labbé, Lauren LeBon, Bryan King, Ngoc Vu, Emily H. Stoops, Nina Ly, Austin E. Y. T. Lefebvre, Phillip Seitzer, Swathi Krishnan, Jin-Mi Heo, Bryson Bennett () and Carmela Sidrauski ()
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Katherine Labbé: Calico Life Sciences LLC
Lauren LeBon: Calico Life Sciences LLC
Bryan King: Calico Life Sciences LLC
Ngoc Vu: Calico Life Sciences LLC
Emily H. Stoops: Calico Life Sciences LLC
Nina Ly: Calico Life Sciences LLC
Austin E. Y. T. Lefebvre: Calico Life Sciences LLC
Phillip Seitzer: Calico Life Sciences LLC
Swathi Krishnan: Calico Life Sciences LLC
Jin-Mi Heo: Calico Life Sciences LLC
Bryson Bennett: Calico Life Sciences LLC
Carmela Sidrauski: Calico Life Sciences LLC

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: Abstract The integrated stress response (ISR) enables cells to cope with a variety of insults, but its specific contribution to downstream cellular outputs remains unclear. Using a synthetic tool, we selectively activate the ISR without co-activation of parallel pathways and define the resulting cellular state with multi-omics profiling. We identify time- and dose-dependent gene expression modules, with ATF4 driving only a small but sensitive subgroup that includes amino acid metabolic enzymes. This ATF4 response affects cellular bioenergetics, rerouting carbon utilization towards amino acid production and away from the tricarboxylic acid cycle and fatty acid synthesis. We also find an ATF4-independent reorganization of the lipidome that promotes DGAT-dependent triglyceride synthesis and accumulation of lipid droplets. While DGAT1 is the main driver of lipid droplet biogenesis, DGAT2 plays an essential role in buffering stress and maintaining cell survival. Together, we demonstrate the sufficiency of the ISR in promoting a previously unappreciated metabolic state.

Date: 2024
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DOI: 10.1038/s41467-024-52538-5

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