Quantitative proteomic analysis reveals apoE4‐dependent phosphorylation of the actin regulating protein VASP

Background Apolipoprotein E4 (APOE4) is the major genetic risk factor for Alzheimer’s disease (AD). Current evidence suggests that neuronal expression of apoE4 is sufficient to promote neuropathology via a gain‐of‐function mechanism; however, the precise molecular mechanisms mediating this process are still unclear. To elucidate specific protein targets and cellular pathways dysregulated due to apoE4 expression, we performed global proteomic profiling of ubiquitylation and phosphorylation signaling in Neuro‐2a cells stably expressing either apoE3 or apoE4. Method Neuro‐2a cells (apoE3 or apoE4) were lysed and proteins digested into peptides. Peptides were enriched for either phosphorylation or ubiquitylation post‐translational modifications, and the resulting peptides were detected and quantified using a label‐free quantitative proteomics workflow. Modification sites were detected by MaxQuant, and statistical analysis was performed using MSstats to identify significantly regulated modification sites (p