Fig. 1

Overall strategy to identify potential mechanism underlying HHcy-suppressed Aβ phagocytosis in microglia in AD. We identified differentially expressed genes (DEG) in microglia (MG) from human and mouse Alzheimer’s disease (AD) RNA-seq datasets and performed overlap analysis with our established phagocytosis-related gene lists. This led to the discovery of 326 phagocytic MG DEGs in both human and mouse AD. In addition, we searched a human AD cortex methylome dataset and found 23 hypomethylated phagocytic MG genes in human AD. Furthermore, we performed a PubMed search to identify 431 AD genes from genome-wide association studies (GWAS) and found 20 GWAS-mapped phagocytic AD MG DEGs. To identify the gene targets that mediate the suppression of Aβ phagocytosis in microglia by HHcy in AD, we isolated MG from Cbs-/- and control mice and performed bulk RNA-seq. We used the identified 353 HHcy-altered MG DEGs to overlap with the three gene lists mentioned above, resulting in the identification of three final gene lists: HHcy-altered phagocytic AD MG DEGs (10 genes), HHcy-altered hypomethylated phagocytic AD MG DEGs (1 gene), and HHcy-altered GWAS-mapped phagocytic AD MG DEGs (1 gene), which was used to establish the hypothetic model for potential mechanism underlying HHcy-suppressed Aβ phagocytosis in microglia in AD. Aβ, amyloid beta; AD, Alzheimer’s disease; Cbs, cystathionine beta synthase; DEGs, differentially expressed genes; DMG, differentially methylated gene; MG, microglia; HHcy, hyperhomocysteinemia