Identification of key targets and potential mechanisms underlying microglia dysfunction in Alzheimer’s disease based on single-cell transcriptomics and Mendelian randomization

The function of key regulatory genes in shaping the immune microenvironment of Alzheimer's disease (AD) remains elusive. Thus, this investigation aimed to detect key targets and potential mechanisms underlying microglia dysfunction in AD based on GWAS and single-cell transcriptomics.

The present investigation utilized single-cell RNA sequencing (scRNA-seq) with microarray data (GSE243292 and GSE53697) to uncover cellular subtypes and critical regulatory genes linked to AD. Differential gene expression analysis, Mendelian randomization (MR), and immune cell infiltration profiling were performed to identify potential causal genes and their biological pathways. Additionally, miRNA and transcription factor network analyses were conducted to explore gene regulation. Lastly, functional pathway enrichment analysis and correlation studies with AD-related genes were conducted to assess biological significance. This study was conducted without using artificial intelligence (AI) tools in accordance with the TITAN Guidelines 2025.

The findings of scRNA-seq analysis yielded 8 distinct cell subtypes, with microglia being significantly enriched in AD samples. Marker genes of microglia were correlated with pathways like glutamate receptor signaling and actin filament-based processes. Moreover, MR analysis identified EPB41L2, INPP5D, and ZFHX3 as key genes influencing AD risk, which were significantly associated with immune cells like T and B cells. Meanwhile, functional pathway analysis revealed enrichment in the NF-kappa B, TNF signaling, and PI3K-Akt pathways. Finally, miRNA and transcription factor analyses uncovered shared regulatory mechanisms, while correlations with genes such as PSEN1 and NPC1 validated their association with the pathogenesis of AD.

This investigation offers a new understanding of the immune landscape of AD by identifying key genetic regulators and their associated immune pathways.