Fig. 7

hiMG after chronic Aβ treatment are a heterogeneous cell population of microglia and macrophage-like cells mimicking AD. A The subset of hiMG generated from cell cluster 13 (Fig. 5A) from the 5w Aβ hiNS(+) data set reveals three distinct sub-clusters (13a-c). B Overlay examples are shown for each cluster of hiMG. C Gene ontology analysis suggests different biological properties of each cluster. D Volcano plots of DEGs with highlighted genes of interest, including APOE in cluster 1 of DAM-like microglia. E Cytokine levels in hiNS concentrated supernatant of all experimental conditions measured via multiplex ELISA (N = 3; pooled supernatant from six individual hiNS each). In all hiNS(−) samples, cytokine levels were mostly undetectable or low. Cytokine production increases in hiNS(+) in ctrl and Aβ treated hiNS with IL- 6 and IL- 12 levels significantly increased from ctrl hiNS(+) to 5w Aβ hiNS(+). Statistical testing performed using two-way ANOVA followed by Holm-Sidak post-hoc tests on logarithmically transformed data. F Ligand-receptor interaction analysis between hiMG ligands paired with receptors on astrocytes and neurons in 5w Aβ hiNS(+). Differentially expressed ligands of microglia/macrophages (cluster 13) and differentially expressed receptors on astrocytes (cluster 0) or neuronal cell populations (all neuronal clusters pooled) were identified and ligand-receptor (mean expression > 10%) pairs were matched and plotted against each other. Genes of interests are highlighted in color.