Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation

Mechanistic or mammalian target of rapamycin complex 1 (mTORC1) is an important regulator of effector functions, proliferation, and cellular metabolism in macrophages. The biochemical processes that are controlled by mTORC1 are still being defined. Here, we demonstrate that integrative multiomics in conjunction with a data-driven inverse modeling approach, termed COVRECON, identifies a biochemical node that influences overall metabolic profiles and reactions of mTORC1-dependent macrophage metabolism. Using a combined approach of metabolomics, proteomics, mRNA expression analysis, and enzymatic activity measurements, we demonstrate that Tsc2, a negative regulator of mTORC1 signaling, critically influences the cellular activity of macrophages by regulating the enzyme phosphoglycerate dehydrogenase (Phgdh) in an mTORC1-dependent manner. More generally, while lipopolysaccharide (LPS)-stimulated macrophages repress Phgdh activity, IL-4-stimulated macrophages increase the activity of the enzyme required for the expression of key anti-inflammatory molecules and macrophage proliferation. Thus, we identify Phgdh as a metabolic checkpoint of M2 macrophages. [Display omitted] •Metabolomics and inverse modeling reveal a Tsc2/mTORC1-dependent checkpoint in macrophages•M2 macrophages have high Phgdh activity•Phgdh activity promotes M2 polarization•Phgdh activity supports macrophage proliferation Wilson et al. show that Tsc2, a negative regulator of mTORC1 signaling, critically influences the metabolome of macrophages. Inverse data-driven modeling and multiomics data reveal that Phgdh is an mTORC1-dependent metabolic checkpoint of macrophage proliferation and polarization. Phgdh is required for the expression of key anti-inflammatory molecules and M2 proliferation.