Comprehensive Reconstruction and Manipulation of the Pluripotent Stem Cell Metabolic Network

Metabolism is an emerging stem cell hallmark tied to cell fate, pluripotency and self-renewal. Yet systems-level understanding of stem cell metabolism has been limited by the lack of genome-scale network models. Here we develop a systems approach to integrate time-course extracellular and intracellular metabolomics data with a computational model of metabolism to reconstruct the metabolic state of naïve- and primed- murine embryonic stem cells that have different development potential, and discovered three key insights. First, alterations in one-carbon metabolism involving phosphoglycerate dehydrogenase, folate and nucleotide metabolism are key pathways that differ between the two states, resulting in differential sensitivity to folate inhibitors. Second, the model predicted that the master regulator Lin28 regulates this one-carbon metabolic pathway associated with pluripotency. Third, we identified and validated metabolic reactions such as Adenosylhomocysteinase, that can differentially impact histone methylation in naïve and primed cells. Our network-based approach provides a framework for characterizing stem cell metabolism for rational cellular engineering.