Acetyl-CoA Homeostasis via Mitochondrial Pyruvate Oxidation Governs Survival, Transcriptional Fidelity and Neural Specification in Primed Human Embryonic Stem Cells

Human embryonic stem cells (hESCs) hold immense promises for regenerative medicine and exhibit two distinct pluripotency states: primed and naïve. However, metabolic regulation underlying these states remains incompletely understood. In particular, mitochondrial pyruvate oxidation in pluripotency regulation has not been documented. Here, we combined an inducible dihydrolipoamide S-acetyltransferase (DLAT) knockout model and pharmacological inhibition of mitochondrial pyruvate uptake (via the mitochondrial pyruvate carrier inhibitor UK5099) to dissect the state-specific effects of mitochondrial pyruvate oxidation in isogenic naïve and primed hESCs. Primed hESCs lacking DLAT or treated with UK5099 displayed pronounced cell death, reduced global protein acetylation levels, and transcriptional dysregulation. These defects were partially rescued by sodium acetate supplementation, implicating a reduction in acetyl-CoA abundance as a key mechanism. Notably, a set of neural lineage genes was specifically downregulated by disrupted mitochondrial pyruvate oxidation in primed hESCs, revealing the importance of mitochondrial pyruvate oxidation–mediated acetyl-CoA production in priming neural differentiation. In line with this, disruption of mitochondrial pyruvate oxidation impaired the differentiation process of primed hESCs towards neuroectoderm. In contrast, DLAT depletion in naïve hESCs did not affect cell growth and the naïve pluripotency state, highlighting the pluripotency state-dependent function of mitochondrial pyruvate oxidation. Our study uncovers the pivotal roles of mitochondrial pyruvate oxidation-mediated acetyl-CoA production for sustaining survival and transcriptional fidelity as well as facilitating neural differentiation in primed hESCs. Moreover, we emphasize that the function of mitochondrial pyruvate oxidation in hESCs is pluripotency state-dependent. These findings provide new cues for optimizing hESC maintenance and differentiation through targeted metabolic manipulation. © 2026 Wiley Periodicals LLC.