Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer’s disease heterogeneity

The molecular correlates of Alzheimer’s disease (AD) are increasingly being defined by omics. Yet, the findings from different data types or cohorts are often difficult to reconcile. Collecting multiple omics from the same individuals allows a comprehensive view of disease-related molecular mechanisms, while addressing conflicting findings derived from single omics. Such same-sample multi-omics can reveal, for instance, when changes observed in the transcriptome share distinct but coordinated signals in epigenetics and proteomics, relationships otherwise unclear. Here, we apply a data-driven multi-omic framework to integrate epigenomic, transcriptomic, proteomic, metabolomic, and cell-type-specific population data from up to 1,358 aged human brain samples from the Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP). We demonstrate the existence of sprawling cross-omics cross-system biological factors that also relate to AD phenotypes. The strongest AD-associated factor (factor 8) involved elevated immune activity at the epigenetic level, decreased expression of heat shock genes in the transcriptome, and disrupted energy metabolism and cytoskeletal dynamics in the proteome. We also showed immune-related factors (factors 2 and 3) with discordant enrichments, reflecting reactive-like glial subpopulations and protective contributions from surveillance microglia. Both were negatively associated with AD pathology, suggesting potential immune resilience mechanisms. Finally, unsupervised clustering of participants revealed eleven molecular subtypes of the aging brain, including three clusters strongly associated with AD but displaying distinct molecular signatures and phenotypic characteristics. Our findings provide a comprehensive map of molecular mechanisms underlying AD heterogeneity, highlighting the complex role of neuroinflammatory processes, and yielding potential novel biomarkers and therapeutic targets for precision medicine approaches to AD treatment.