Dynamic functional connectivity and transcriptomic signatures reveal stage-dependent brain network dysfunction in Alzheimer's disease spectrum.

BACKGROUND: Alzheimer's Disease Spectrum (ADS) progresses from preclinical stages to dementia, with dynamic functional connectivity (dFC) changes emerging early. This study aimed to investigate the dynamic changes in brain networks across different stages of ADS and their underlying molecular mechanisms. METHODS: This cross-sectional study included 239 participants: 69 Healthy Controls (HC), 83 with Subjective Cognitive Decline (SCD), 56 with Mild Cognitive Impairment (MCI), and 31 with Alzheimer's disease (AD). All participants underwent neuropsychological testing and resting-state functional magnetic resonance imaging (rs-fMRI). Leading Eigenvector Dynamics Analysis (LEiDA), a data-driven method that captures time-resolved whole-brain dFC, was applied to identify transient brain states and calculated their occupancy rate, dwell time, and transition probabilities. Group differences in these dynamic metrics were assessed using a General Linear Model (GLM), and their correlations with cognitive performance were examined. To explore the molecular basis of significant dFC alterations, we performed gene-category enrichment analysis. This analysis integrated the spatial maps of altered brain states with regional gene expression data from the Allen Human Brain Atlas (AHBA), using spin permutations to ensure statistical robustness. RESULTS: We identified ten recurring brain states and characterized how their transition patterns, stability, and frequency differed as a function of disease severity. Specifically, early disruptions appeared as altered transition probabilities between states, while later stages showed pronounced changes in the dwell time and occurrence rates of specific states, closely associated with cognitive decline. Notably, one brain state marked by synchronized activity in attention, salience, and default mode networks emerged as a critical hub linked to both cognitive deterioration and excitatory-inhibitory imbalance. Genes associated with this state were enriched in glycine-mediated synaptic pathways and expressed in both excitatory and inhibitory neurons, showing spatial and temporal patterns that extended from early development into late disease stages. CONCLUSIONS: Our study uncovered the stage-dependent dFC changes and their molecular underpinnings of brain network dysfunction across the ADS.