Transcriptomic analysis reveals and validates lipid raft–associated biomarkers and functional networks in Alzheimer’s disease
Alzheimer’s disease (AD) involves complex changes, including synaptic dysfunction, neuroinflammation, and metabolic impairment, yet the role of lipid raft–associated gene networks in these processes remains unclear. In this study, we performed an integrative transcriptomic analysis using the GSE5281 dataset and validated the findings in an independent cohort (GSE33000). By combining differential expression analysis with weighted gene co-expression network analysis, we identified 72 lipid raft–associated genes linked to mitochondrial, synaptic, and immune-related pathways. Using network analysis and machine learning approaches (LASSO and SHAP), we further identified eight key biomarkers (CBL, CD44, EZR, FAS, FYN, ITGB1, MAPK1, and TGFBR1) that showed strong diagnostic performance and consistent results across datasets. Functional analysis revealed increased inflammatory signaling, including pyroptosis and cytokine pathways, alongside reduced oxidative phosphorylation and synaptic activity. Interestingly, immune profiling showed only minor differences in immune cell infiltration, but clear activation of multiple immune pathways, such as Th2 and Treg signaling, CD8⁺ T-cell signatures, and IL-6/IL-10–mediated inflammation. These immune changes were strongly associated with lipid raft–related biomarkers. Overall, our findings suggest that lipid raft dysregulation may act as a key link between immune activation, mitochondrial dysfunction, and synaptic impairment in AD.