Transcriptome-informed metabolic modeling reveals astrocyte-specific vulnerabilities in mild cognitive impairment and Alzheimer’s disease progression

Introduction Astrocytes are essential for maintaining neuronal homeostasis, yet their stage-specific contribution to mild cognitive impairment (MCI) and Alzheimer’s disease (AD) remains insufficiently understood. This study aimed to investigate astrocyte-associated transcriptional and metabolic alterations across the control-MCI-AD continuum using integrated transcriptomic and genome-scale metabolic modeling approaches. Methods Transcriptomic profiles from hippocampal CA1 tissue (GSE28146) were analyzed across four clinical conditions (control, early MCI, advanced MCI, and AD). Astrocyte-associated expression programs were inferred using the unsupervised deconvolution algorithm CDSeq and validated through canonical marker enrichment, correlation with external reference signatures, and comparison with an independent single-nucleus RNA-seq astrocyte pseudobulk dataset. The inferred profiles were integrated into a curated human astrocyte genome-scale metabolic model to generate condition-specific models, which were analyzed using flux balance analysis (FBA) and flux variability analysis (FVA). Results The analyses supported stage-dependent remodeling of astrocyte-associated transcriptional and metabolic programs during disease progression. Early MCI was associated with signaling and stress-adaptation changes, whereas advanced MCI and AD showed broader disruption of synaptic support, redox homeostasis, and inflammatory-related programs. Model predictions indicated a progressive reduction in a biomass-derived maintenance proxy from control to advanced MCI, followed by a partial rebound in AD, suggesting a compensatory shift toward reactive-like astrocyte states rather than full functional recovery. Flux variability analysis revealed reduced metabolic flexibility across disease stages, particularly in glutamate-glutamine cycling, glutathione/redox metabolism, glycolysis-pyruvate metabolism, cholesterol handling, and one-carbon/folate metabolism. Discussion These findings support the view that astrocytes undergo progressive, stage-specific metabolic reprogramming during the transition from healthy aging to AD. Early alterations in redox regulation, neurotransmitter cycling, and mitochondrial function may contribute to early neuronal vulnerability. This work highlights astrocyte-centered pathways as potential targets for future experimental validation and therapeutic exploration.