Cross‐Platform Synaptic Network Analysis of Alzheimer’s Disease Contextualizes Proteomic Targets for Functional Validation

Abstract

AbstractBackgroundCognitive decline in Alzheimer’s disease (AD) correlates well with the extent of tau pathology and synapse or dendritic spine loss. Thus, studying synaptic processes may aid in the identification of new therapeutic targets that limit cognitive decline. The entorhinal cortex (EC) is an initial site of tau tangle formation, from which tau can propagate to other brain regions through synaptic connections. We developed a pipeline whereby dendritic spine density and morphology as well as synaptic tau measurements from the EC were incorporated into a synaptic proteomic network to identify mechanisms of synaptic pathology in AD patients.MethodGolgi‐stained dendrites from postmortem human BA28 EC were imaged using high‐resolution brightfield microscopy and digitally reconstructed in 3D for morphometric analysis. Synaptosome fractions were isolated from the same BA28 samples. Levels of synaptosome and insoluble phosphorylated tau were measured by ELISA. Additionally, liquid chromatography coupled with tandem mass spectrometry‐based proteomics was performed on synaptosomes. Weighted Gene Co‐Expression Network Analysis (WGCNA) was used to generate a synaptic network of protein co‐expression modules. Module expression was correlated with dendritic spine measurements and phospho‐tau levels to guide selection of proteins for validation in model systems. Validation experiments were performed in neurons and Neuro‐2a cells, using a CRISPR activation system for target gene upregulation.ResultSpine density in the EC is reduced in AD, but not in cognitively normal individuals with AD pathology (CAD) cases. AD cases exhibit more synaptosomal pS396 tau than CAD cases. Module expression was correlated with dendritic spine density and morphology. We identified TWF2 as a hub protein of Module 16, which is positively correlated with thin spine length. Twf2 upregulation increased thin spine length in cultured neurons. Module expression was then correlated with phospho‐tau levels. We identified PPP1R7 as a hub protein of Module 24, which is inversely correlated with synaptosomal pS396 tau in human EC.ConclusionWe demonstrate that incorporating orthogonal cellular and molecular measurements into a proteomic network enables unbiased identification of proteins functionally involved in regulating those traits. Beyond elucidating synaptic processes in AD, this pipeline offers a blueprint to better contextualize omics‐based targets with relevant biological mechanisms.