Fig. 6

snRNA-seq on hiNS(−/+) in ctrl, 3w and 5w Aβ conditions reveals a hiMG-dependent astrocyte AD-like transcriptional profile in 3w/5w Aβ hiNS(+). A Merged UMAP of all 6 experimental groups displaying cell clusters and cell type identification. B Split merged UMAPs without hiMG (left) and with hiMG (right). Note the lack of a microglial population in hiNS(−), reduced neuronal populations in the absence of microglia indicating severe cell loss after 5w Aβ treatment. C Total cell counts of annotated cell types per experimental condition. D Isolated astrocyte population in a merged UMAP displaying four distinct clusters. E Data set of origin for all 6 conditions illustrating significant shifts of astrocyte gene expression depending on Aβ treatment and hiMG presence. Dashed lines mark the rough outline of the predominantly 3w/5w Aβ hiNS(+) astrocyte populations. F Number of astrocytes sorted per sub-cluster. Note that astrocyte numbers varied between conditions with 5w Aβ hiNS(+) marking the largest astrocyte population. G Heatmap of differentially expressed genes selected from direct comparison between 5w Aβ hiNS(+) and ctrl hiNS(+) astrocytes. Note that upregulation of genes with Aβ treatment required the presence of hiMG, including APOE. H Overlay examples of AD-associated gene expression in astrocytes in 5w Aβ hiNS(+) astrocytes. I Gene ontology analysis of ctrl hiNS(+) and 5w Aβ hiNS(+) astrocyte groups highlight distinct hiMG-dependent phenotypical differences in Aβ treated astrocytes. Direct comparison of DEGs depending on hiMG in 3w (J) and 5w (K) Aβ treated hiNS shown in volcano plots (compared in pairs). Genes of interest are labeled. Note that many AD-associated genes, such as GFAP, VIM and APOE, are only upregulated if hiMG were present during Aβ treatment