Additional file 1 of Identification of methylation-regulated genes modulating microglial phagocytosis in hyperhomocysteinemia-exacerbated Alzheimer’s disease

Additional file 1: Supplemental Figure S1. Functional-validated human/mouse Aβ phagocytic AD MG DEGs with opposing changes in gene expression in human/mouse AD MG and mouse Aβ+ MG (14 genes). A total of 14 functional-validated human Aβ phagocytic AD MG DEGs were identified by overlapping functional-validated human AD MG DEG with mouse Aβ+ MG screening dataset, displaying opposite changes in gene expression. Abbreviation: Aβ, amyloid beta; AD, Alzheimer’s disease; DEG, differentially expressed gene; FC, fold change; MG, microglia. Supplemental Figure S2. Identification of GWAS-mapped phagocytic AD MG DEGs altered by HHcy. (A) Identification of 431 GWAS-mapped AD genes. A summary diagram was created to establish a set of AD genes mapped by GWAS using a PubMed search. (B) GWAS-mapped AD MG DEGs (43). We identified 43 GWAS-mapped AD MG DEGs by overlapping 431 GWAS-mapped AD genes with 409 human and 777 mouse AD MG genes. Among the 43 genes, 4 were common to both species. We plotted the expression changes of these genes in AD MG using a histogram, where the dark red bars indicate genes that were identified in both human (C) and mouse (D) AD MG. (E) Network and neuro-immunological AD biological process. We used the 43 identified GWAS-mapped AD MG genes to perform Gene Ontology (GO) analysis and identify the top 15 neuro-immunological biological processes and molecular networks. (F) GWAS-mapped phagocytic AD MG DEGs altered by HHcy. GWAS-mapped phagocytic AD MG genes altered by HHcy were identified by overlapping 431 human GWAS-mapped AD genes with 326 phagocytic AD MG genes and 353 Cbs-/- MG genes. The functions and cellular locations of these genes are described in a table. Abbreviation: Aβ, amyloid beta; AD, Alzheimer’s disease; CI, confidence interval; DEG, differentially expressed gene; ER, endoplasmic reticulum; FC, fold change; FDR, false discovery rate; GO, gene ontology analysis; GWAS, Genome-wide association studies; HHcy, hyperhomocysteinemia; MG, microglia; PM, plasma membrane; TGN, trans-Golgi-network.