Integrative SMR prioritizes oxidative stress–related regulatory genes for Alzheimer’s disease with brain-tissue validation

TL;DR

This study identifies oxidative stress-related genes linked to Alzheimer's disease using genetic and epigenetic data, highlighting potential therapeutic targets.

Contribution

A novel three-step SMR framework integrates GWAS, eQTL, and mQTL data to prioritize oxidative stress-related genes in Alzheimer’s disease.

Findings

Candidate genes like CRLS1, PRKAA1, and APP are associated with Alzheimer’s disease risk.

KEAP1, SIRT1, and PRDX5 show brain-tissue relevance in AD.

Epigenetic sites like cg20211653 are linked to transcriptional mechanisms in AD.

Abstract

Oxidative stress (OS) plays a critical role in the pathogenesis of Alzheimer’s disease (AD), yet its genetic and epigenetic regulatory mechanisms remain unclear. In this study, we applied a three-step summary-based Mendelian randomization (SMR) framework to integrate Alzheimer’s disease (AD) GWAS summary statistics with peripheral-blood eQTL and mQTL datasets, and further evaluated brain-tissue relevance using GTEx v8 and AMP-AD resources. Across the three-step SMR analyses, we prioritized multiple OS-related candidate genes (e.g., CRLS1, PRKAA1, CYP2E1, GPX1, and APP) associated with AD risk, and brain-tissue analyses further highlighted KEAP1, SIRT1, and PRDX5 as region-relevant signals. Functional enrichment analyses highlighted critical pathways such as "Nrf2-mediated antioxidant response" and "PI3K-AKT signaling," emphasizing the roles of oxidative stress, mitochondrial function, and neuroinflammation in AD. Novel regulatory mechanisms were uncovered at methylation sites (e.g., cg20211653 associated with ABCA1), linking epigenetic regulation to transcriptional mechanisms and providing candidates for brain-tissue follow-up. This study provides new insights into the molecular underpinnings of AD, bridging genetic variation, epigenetic regulation, and transcription, and identifies potential therapeutic targets for mitigating oxidative damage and neurodegeneration.

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