Identification of methylation-regulated genes modulating microglial phagocytosis in hyperhomocysteinemia-exacerbated Alzheimer's disease

Background Hyperhomocysteinemia (HHcy) has been linked to development of Alzheimer's disease (AD) neuropathologically characterized by the accumulation of amyloid beta (A beta). Microglia (MG) play a crucial role in uptake of A beta fibrils, and its dysfunction worsens AD. However, the effect of HHcy on MG A beta phagocytosis remains unstudied.Methods We isolated MG from the cerebrum of HHcy mice with genetic cystathionine-beta-synthase deficiency (Cbs(-/-)) and performed bulk RNA-seq. We performed meta-analysis over transcriptomes of Cbs(-/-) mouse MG, human and mouse AD MG, MG A beta phagocytosis model, human AD methylome, and GWAS AD genes.Results HHcy and hypomethylation conditions were identified in Cbs(-/-) mice. Through Cbs(-/-) MG transcriptome analysis, 353 MG DEGs were identified. Phagosome formation and integrin signaling pathways were found suppressed in Cbs(-/-) MG. By analyzing MG transcriptomes from 4 AD patient and 7 mouse AD datasets, 409 human and 777 mouse AD MG DEGs were identified, of which 37 were found common in both species. Through further combinatory analysis with transcriptome from MG A beta phagocytosis model, we identified 130 functional-validated A beta phagocytic AD MG DEGs (20 in human AD, 110 in mouse AD), which reflected a compensatory activation of A beta phagocytosis. Interestingly, we identified 14 human A beta phagocytic AD MG DEGs which represented impaired MG A beta phagocytosis in human AD. Finally, through a cascade of meta-analysis of transcriptome of AD MG, functional phagocytosis, HHcy MG, and human AD brain methylome dataset, we identified 5 HHcy-suppressed phagocytic AD MG DEGs (Flt1, Calponin 3, Igf1, Cacna2d4, and Celsr) which were reported to regulate MG/M Phi migration and A beta phagocytosis.Conclusions We established molecular signatures for a compensatory response of A beta phagocytosis activation in human and mouse AD MG and impaired A beta phagocytosis in human AD MG. Our discoveries suggested that hypomethylation may modulate HHcy-suppressed MG A beta phagocytosis in AD.

Automated summary

This study investigated the effect of hyperhomocysteinemia (HHcy) on the phagocytosis of amyloid beta (A beta) by microglia (MG) in Alzheimer's disease (AD). Transcriptome analysis revealed that HHcy suppressed A beta phagocytosis by MG and identified key genes involved in this process.