APOE4 copy number‐dependent Complement Pathway Dysregulation

Abstract

AbstractBackgroundComplement has been implicated in the pathophysiology of AD based on human genetic studies, human post‐mortem pathology, and mouse genetic studies. However, the relationship between complement activation and other AD risk factors (such as the APOE4 allele) remains unclear.MethodWe used pathway analysis of the ADNI targeted proteomics dataset to identify protein clusters highly correlated with each other, including a complement pathway cluster. We then developed a hybrid proteomics platform, which allows for both discovery proteomics (via LC‐MS/MS) and precise quantitation of complement protein‐derived peptides via Stable Isotope Labelled (SIL) internal control peptides for the complement proteins. We then tested this hybrid proteomics platform on over 130 CSF samples from cognitively normal older adults (ages 60‐80), together with assays for CSF amyloid beta, tau and p‐tau‐181p. Spearman correlation tests were used to evaluate correlations between protein pathway expression and demographic variables, such as APOE4 allele number.ResultPathway analysis of the ADNI targeted proteomics dataset identified a cluster of complement proteins whose levels were highly correlated with each other in the CSF; this cluster included peptides from C1QB, C2, C3, C4A, C5, C6, C8B and CRP and several additional proteins. Across ∼300 individuals (including cognitively normal controls, MCI and AD patients), expression of this complement protein cluster was inversely correlated with APOE4 allele count and gender (with lower expression in females), and a positive correlation with age (P<0.05 for each). To further study complement protein levels in human CSF across the AD spectrum, we developed a hybrid proteomics platform for precise quantitation of complement proteins and for unbiased discovery proteomics. In 130 CSF samples from older adults, we were able to detect ∼9,000 different peptides from 884 different proteins, and to precisely quantitate all proteins in the classical, alternative and mannose binding lectin complement pathways using the SIL peptide internal controls. Here we report data on APOE4 copy number dependent changes in quantified CSF complement protein levels, and on APOE4 dependent changes across the human CSF proteome.ConclusionAPOE4 is associated with a reduction in CSF complement protein levels, which may reflect increased complement pathway activation and ensuing degradation of these proteins.