Protein phosphatase 2A, complement component 4, and APOE genotype linked to Alzheimer’s disease using a systems biology approach

Background: Recent reports suggest that the rare apolipoprotein E (APOE) Christchurch mutation and ɛ2 allele protect against Alzheimer disease (AD) pathology by reducing the burden of tau pathology. However, the mechanism(s) underlying the ɛ2 protective effect linking to tau is largely unknown. Methods: The role of the ɛ2 allele in AD was investigated a genome-wide association study (GWAS) for AD among 2,120 ɛ2 carriers from the Alzheimer Disease Genetics Consortium (ADGC), and then prioritized by gene network analysis, differential gene expression analysis at tissue- and cell-levels as well as methylation profiling of CpG sites, in prefrontal cortex tissue from 761 brains of the Religious Orders Study and Memory and Aging Project (ROSMAP) and the Framingham Heart Study (FHS), Boston University Alzheimer Disease Center (BUADC). The levels of two catalytic subunit proteins from protein phosphatase 2A (PPP2CA and PPP2CB) were validated in prefrontal cortex area of 193 of the FHS/BUADC brains. The findings from human autopsied brains were further validated by a co-culture experiment of human isogenic APOE induced pluripotent stem cell (iPSC) derived neurons and astrocytes. Results: Of the significantly associated loci with AD among APOE ɛ2 carriers (P<10-6), PPP2CB (P=1.1x10-7) was the key node in the APOE ɛ2-related gene network and contained the most significant CpG site (P=7.3x10-4) located 2,814 base pair upstream of the top-ranked GWAS variant. Among APOE ɛ3/ɛ4 subjects, the level of Aβ42 was negatively correlated with protein levels of PPP2CA (P=9.9x10-3) and PPP2CB (P=2.4x10-3), and PPP2CA level was correlated with the level of pTau231 level (P=5.3x10-3). Significant correlations were also observed for PPP2CB with complement 4B (C4B) protein levels (P=3.3x10-7) and PPP2CA with cross reactive protein (CRP) levels (P=6.4x10-4). C1q level was not associated with Aβ42, pTau231, PPP2CB, or C4B levels. We confirmed the significant correlation of PPP2CB expression with pTau231/tTau ratio (P=0.01) and C4A/B (P=2.0x10-4) expression observed in brain tissue in a co-culture experiment of iPSC derived neurons and astrocytes. Conclusion: We demonstrated for the first time a molecular link between a tau phosphatase and the classical complement pathway, especially C4, and AD-related tau pathology.