Fig. 1

Human iPSC-derived mixed cell type neurospheres (hiNS) are comprised of neurons and glia. A A single female human iPSC line was used to generate neuronal precursors step prior to hiNS formation. The same iPSC cells were used to differentiate microglia-like cells (hiMG). B Schematic of hiNS generation and infiltration of hiMG to form mature hiNS. hiNS after hiMG infiltration are defined as hiNS(+) while labeled hiNS(−) in the absence of hiMG. C Single nuclei RNA sequencing (snRNA-seq) on hiNS(±). Overview of identified cell clusters and cell type identification in a merged data set of both groups D Expression pattern of genes across cell populations for neuronal, astrocytic and microglia/macrophage displaying example marker genes. E Datasets of origin confirming the presence of microglia/macrophage (marked in blue) is exclusive to hiNS(+) and that astrocyte gene expression (marked in red) appears shifted by the presence of hiMG. F UMAP of isolated astrocyte populations from both data sets reveals 3 distinct sub-clusters with clusters 0b and 0c predominantly in hiNS(+) astrocytes and cluster 0a preferentially in hiNS(−) astrocytes. G Analysis of the dataset of origin illustrating the shift in astrocyte gene expression in the presence of microglia. H Pearson correlation (r = 0.978) confirms the close similarities between the two astrocyte populations. I Differential gene expression (DEGs) pattern of a selection of DEGs shown in heatmaps. J Gene ontology analysis of astrocyte clusters with and without hiMG