Impact of APOE e3 and e4 genotypes on plasma proteome signatures in Alzheimer's disease

The {varepsilon}4 allele of the apolipoprotein E (APOE) gene is a high-risk factor for Alzheimers disease (AD). However, approximately 25%-40% of patients with AD do not carry the APOE{varepsilon}4 allele, and the pathophysiological mechanisms underlying AD are less evident in these individuals. The main objective of this study was to understand better the changes in plasma that may contribute to disease pathogenesis in AD and how APOE{varepsilon}3 and APOE{varepsilon}4 contribute to biomarker profiles in AD. We conducted an in-depth plasma proteomics analysis using intensive depletion of high-abundant plasma proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 14 (Hu14) followed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS PAGE) technique. In this study, we identified a high number of protein expression alterations in plasma which were found uniquely in APOE{varepsilon}3 and APOE{varepsilon}4 carriers. These differentially expressed proteins (DEPs) were associated with several molecular functions, including complement cascade, glycolysis, metabolism, plasma lipoprotein assembly, remodelling, and clearance. In addition to unique changes in both APOE genotypes, many proteins were also dysregulated in the presence of both APOE{varepsilon}3 and APOE{varepsilon}4 genotypes depicting the involvement of these proteins in the pathogenesis of AD regardless of the APOE genotypes. We also compared the plasma proteomes of{varepsilon} 4 and{varepsilon} 3 carriers in normal controls, which provided insight into factors that may provide protection from progression to AD despite the presence of the{varepsilon} 4 allele. Furthermore, our findings also identified some proteins previously discovered in AD CSF and brain proteomics signatures that could provide clinically meaningful information.