Integrated Multi-Omics Analysis and Cross-Model Validation Reveal Mitochondrial Signatures in Alzheimer's Disease

Alzheimer's disease (AD) is a devastating neurodegenerative disorder where mitochondrial dysfunction is increasingly recognized as pivotal, yet its comprehensive molecular underpinnings remain incompletely understood. This study aimed to systematically identify and validate mitochondria-related biomarkers associated with AD risk and brain resilience, thus elucidating the molecular mechanisms underpinning mitochondrial dysfunction in AD.

We innovatively integrated a multi-omics approach, encompassing genomics, DNA methylation, RNA-sequencing, and miRNA profiles from the ROSMAP and ADNI cohorts (sample sizes ranging from 638 to 2090 per omic layer). Additionally, we applied 10 distinct machine learning methods to robustly identify and validate critical mitochondrial biomarkers relevant to AD progression. Subsequent validation was performed using a two-tiered approach: an in vivo AD mouse model to establish phenotypic relevance and an in vitro H₂O₂-induced oxidative stress model in HT22 cells to provide direct mechanistic validation.

Our computational analyses identified key biomarkers such as hsa-miR-129-5p and SLC6A12 as pivotal regulators and highlighted the importance of the tricarboxylic acid (TCA) cycle. Experimentally, our AD mouse model exhibited significant cognitive deficits and brain remodeling, linked to a specific transcriptomic signature. Our in vitro model functionally recapitulated mitochondrial dysfunction and oxidative stress. Crucially, a cross-model analysis revealed a core signature of seven genes (including APOE, CDKN1A, and CLOCK) consistently dysregulated in both the cognitively impaired mouse brain and in neuronal cells subjected to direct oxidative insult. This provides powerful functional evidence linking our computationally derived targets, such as mitochondrial-epistatic genes (CLOCK), to AD-relevant pathology.

These functionally validated findings provide deeper insights into the complex mitochondrial regulatory mechanisms involved in AD pathogenesis, offering robust biomarkers and novel potential avenues for developing targeted therapeutic strategies to address this challenging neurodegenerative disease.