DE pathway analysis (Supplementary Table 5) revealed the enrichment of KEGG pathways related to cAMP signaling, synaptic function and long-term potentiation in microglia subcluster 4 (Extended Data Fig. 8e) and an enrichment of KEGG pathways related to general neurodegeneration, AD and other neurodegenerative diseases in subclusters 6 and 8 (Extended Data Fig. 8f,g), suggesting that subcluster 4 represents synaptic-function-supporting microglia and subclusters 6 and 8 represent neuronal APOE4-promoted disease-associated microglia (nE4-DAMs). Here, APOE is linked to neurodegenerative disease.