Fig. 5

Identification of differentially methylated/expressed genes (DM/EG) in hypomethylated phagocytic AD MG. A Endocytic-related AD MG DM/EGs. From a whole-genome DNA methylation dataset (PMID: 33,257,653) in prefrontal cortex (PFC) samples from 1030 Alzheimer’s disease (AD) patients and healthy controls, we identified 559 DM/EG in AD by associating DM-CpG/DMR with altered RNA expression. A total of 16 endocytic-related DM/EGs were identified by overlapping these 559 human AD DM/EGs with 215 endocytosis-related AD MG DEGs. Table describes the epigenetic modification and expression details of these genes in both human and mouse AD MG. B We also identified 14 phagocytic Aβ + AD MG DM/EGs and C 10 phagocytic modifier AD MG DM/EGs, by overlapping the 559 human AD DM/EGs with 377 Aβ + MG DEGs and 286 phagocytic modifier genes, respectively. D A total of 36 phagocytic AD MG DM/EGs are summarized. E Function of 23 hypomethylated phagocytic AD MG DM/EGs. Among the 36 phagocytic AD MG DM/EG, 23 were hypomethylated associated with their gene upregulated (20 genes) and downregulated (3 genes) expression. Aβ, amyloid beta; AD, Alzheimer’s disease; DEG, differentially expressed gene; DMEG, differentially methylated expressed genes; DMR, differentially methylated regions; ER, endoplasmic reticulum; FC, fold change; h, human; m, mouse; MG, microglia; PFC, prefrontal cortex; PM, plasma membrane