AbstractBackgroundWe applied a pseudo‐temporal model to multi‐omic data from individuals with heterogeneous neuropathology to examine molecular changes across the spectrum of Alzheimer’s Disease (AD) progression.MethodsManifold learning algorithms ‘order’ samples based on similarity of expression or abundance patterns to calculate a ‘trajectory’ of disease progression. We applied this approach to RNAseq (N = 1078), TMT‐proteomics (N = 602), and metabolomics (N = 500) profiles of human postmortem brain samples from the ROS/MAP study within the Accelerating Medicine Partnership‐AD consortia (AMP‐AD); 318 individuals were included in all three ‐omics datasets. Analyses were stratified by sex. We examined associations between pseudotime, a quantitative measure of progress along each trajectory, and neuropathological and clinical endpoints. We calculated differential expression or abundance along each trajectory. For transcriptomic and proteomic data, we used gene set enrichment analyses to identify significant GO terms changing along the trajectory and grouped them into 19 distinct AD‐relevant biological domains. We similarly annotated changing metabolic pathways along metabolomic trajectories.ResultsPseudotime estimates were significantly associated with AD status such that “early” (low pseudotime) samples were enriched for controls, and “late” (high pseudotime) samples were enriched for cases, in all ‐omics. Omic‐specific pseudotimes were weakly correlated with each other (Pearson’s r for: RNAseq vs proteomics: 0.39; RNAseq vs metabolomics: 0.28; proteomics vs metabolomics: 0.41). Proteins involved in mitochondrial metabolism and synaptic function were downregulated in early stages in both sexes, while transcriptomic trajectories indicated early sex‐specific differences in synaptic function and immune response. In both sexes, metabolic amino acid and lipid pathways were perturbed in early stages, though specific pathways were different; early Phosphatidylcholine and Leucine, Isoleucine, and Valine Metabolism perturbations were especially prominent in women, while early Glutathione Metabolism perturbations were more prominent in men.ConclusionsDespite differences in the biological nature of the data used to order trajectories, pseudotime was associated with multiple measures of AD progression across all three ‐omics. Each analysis provided a unique snapshot of molecular change across AD progression. Sex‐specific differences, especially those noted early in disease trajectories, may provide crucial insights into key processes driving disease in women and men.