Fig. 1. Study design.

Stage 1: In step 1, aptamer-based proteomics revealed protein-level differences in brain samples from both of two AD cohorts (BLSA and ROS; AD proteomic signature). In step 2, AD proteomic signature proteins were assessed in a cohort of young APOE ε4 carriers and noncarriers (YAPS). Proteins differing in all three cohorts were defined as an incipient AD proteomic signature. In steps 3 and 4, we tested associations between the incipient AD proteomic signature and both AD pathology and antemortem cognitive trajectories. In step 5, we compared GSEA in YAPS to the older adult samples to identify AD-related biologic pathways also altered in young APOE ε4 individuals. Stage 2: In step 6a, we validated a subset of proteins that are targets of approved and experimental drugs for non-AD indications, as biological pathways represented by these proteins may present plausible novel AD therapeutic targets. We assessed their levels in brain tissue using Western blot (WB) in the 3xTg-AD mouse model, as well as in a subset of AD and CN BLSA participants. We additionally assessed subcellular localization using immunohistochemistry (IHC) in brain samples from participants without AD pathology. In step 6b, we validated the incipient AD proteomic signature proteins in three publicly available datasets using orthogonal methods: mass spectrometry (MS)–based human brain proteomics (Mt. Sinai Brain Bank), MS-based mouse brain proteomics (5xFAD transgenic mouse AD model), and a single-cell human neuronal RNA transcriptomic dataset (ROSMAP). In stage 3: we performed phenotypic screening of existing drugs that are FDA-approved or in clinical trials for other indications targeting STAT3, YES1, and FYN in cell culture to test their ability to rescue AD-relevant phenotypes. BLSA, Baltimore Longitudinal Study of Aging; YAPS, Young APOE Postmortem Study; CN, cognitively normal; ROS, Religious Orders Study.