Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells

Pluripotent stem cells (SCs) rely on metabolic rewiring to regulate self-renewal and differentiation. The hexosamine biosynthetic pathway (HBP) integrates multiple metabolic inputs to produce uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), a central substrate for protein and lipid glycoconjugates. While UDP-GlcNAc levels influence pluripotency, the broader metabolic roles of the HBP in stem cell maintenance and differentiation remain largely unexplored. Using proteomic and metabolomic analyses, we uncovered extensive enzymatic remodelling of the HBP during early mouse embryonic stem cell (mESC) differentiation, including a significant decrease in N-acetylglucosamine-6-phosphate (GlcNAc6P) levels, despite stable UDP-GlcNAc levels. Isotope labelling experiments revealed that pluripotent stem cells maintain UDP-GlcNAc biosynthesis through a combination of glucose-driven de novo synthesis and the N-Acetylglucosamine (GlcNAc) salvage pathway, both of which are downregulated during differentiation. Functionally, we identified GlcNAc6P—a point of convergence of the de novo synthesis and the salvage pathways—as a pivotal metabolite of stem cell fate. Preventing GlcNAc6P’s deacetylation by deleting or depleting AMDHD2 impaired mESC differentiation. Mechanistically, we demonstrated that GlcNAc6P catabolism is essential for sustaining cytosolic acetate and in turn acetyl-CoA levels, which are critical for lipid synthesis and histone modifications required for pluripotency exit. These findings establish AMDHD2 as a key supplier of cellular acetate and reveal an essential metabolic link between HBP activity and acetyl-CoA homeostasis. By expanding the role of the HBP beyond UDP-GlcNAc production, this study reveals an unrecognised metabolic vulnerability that can be exploited to manipulate stem cell identity.