Region-specific Transcriptomic Signatures in Alzheimer's Disease: A Meta-analysis of Vulnerable Brain Regions Reveals...

Alzheimer's disease (AD) is characterized by progressive neurodegeneration in regionally vulnerable brain areas, yet molecular insights into early pathogenic mechanisms remain limited.

We conducted a meta-analysis of transcriptomic datasets from brain regions affected in early-to-moderate AD - including entorhinal cortex, CA1 hippocampus, angular gyrus, and frontal cortex synaptoneurosomes - using data from seven mRNA and one microRNA (miRNA) microarray studies (GSE16759, GSE110226, GSE37264, GSE26972, GSE36980, GSE37263, GSE39420, and GSE157239). Preprocessing included background correction, log₂ transformation, quantile normalization, and batch correction via ComBat. Differentially expressed features were defined as false discovery rate <0.05 and | logFC| ≥ 1.23 (genes) or ≥ 2 (miRNAs).

We identified 172 differentially expressed genes (122 upregulated and 50 downregulated) and 82 significant miRNAs. Hub genes included Inositol-trisphosphate 3-kinase B (ITPKB), Synaptotagmin 1, Dystrobrevin alpha (DTNA), X Inactive Specific Transcript, and Regulator of G protein signaling 4 (RGS4). Functional enrichment highlighted calcium signaling, synaptic failure, and neuroinflammation. Notably, hsa-miR-30d-5p was predicted to target both ITPKB and DTNA, suggesting a regulatory axis linking miRNA dysregulation to calcium dyshomeostasis. Receiver operating characteristic analysis revealed that only RGS4 showed moderate discriminative capacity (area under the curve [AUC] =0.70), while other hub genes (e.g., ITPKB, AUC = 0.40) exhibited below-chance performance, underscoring the limitations of single-gene classifiers in postmortem tissue.

This study provides mechanistic hypotheses - rather than diagnostic biomarkers - by uncovering region-specific, miRNA-mediated regulatory networks in AD-affected brain tissues. Future validation in accessible biofluids is essential before clinical translation.