Integrated phenotypic and proteomic screening identifies top‐tier Alzheimer's disease therapeutic targets

INTRODUCTION Alzheimer's disease (AD) is a complex neurodegenerative disorder. Hundreds of therapeutic targets have been nominated through genetic and multi‐omic studies, but effective prioritization remains a major bottleneck. METHODS We applied an integrative screening framework to assess 29 candidate targets from risk‐enriched biological domains. Using disease‐relevant murine BV2 microglial cell lines with stable Psen2 knockdown, we performed small interfering RNA–mediated perturbations followed by cellular phenotypic assays and quantitative proteomics. RESULTS Twenty‐five candidate targets significantly altered at least one phenotype, with stronger effects in Psen2 knockdown cells. Integrated proteomic analyses identified several perturbations that reversed AD‐associated molecular patterns. Five targets—Ap2a2, Pdhb, Pdha1, Dlat, and Psmc3—impacted both phenotypes and related proteomic responses. DISCUSSION We established a scalable platform for target functional validation that bridges unbiased systems‐level assessments of AD risk with experimental evidence. The Emory‐Sage‐Structural Genomics Consortium‐Jax Center Target Enablement to Accelerate Therapy Development for Alzheimer's Disease center will prioritize further resource development for these validated targets. Highlights A screening platform was created to identify the most potent targets from nominated hypotheses. Integrated analysis of cellular proteomics and assay phenotypes was performed. Targets capable of reversing disease‐associated proteomic signal were identified. The most impactful targets were strongly implicated in Alzheimer's disease pathogenesis.