There were nearly 6-fold fewer differentially expressed genes (DEGs) between hiPSC-astrocytes and primary human fetal astrocytes (900 genes) than between hiPSC-astrocytes and isogenic hiPSC-derived neurons (10,000 genes) or NPCs (5,500 genes) (Figures 2C and S2B). hiPSC-astrocytes are highly similar to primary human fetal astrocytes (r = 0.945); the majority of both expressed genes (counts per million [CPM] > 1) and enriched genes (CPM > 5) were shared between hiPSC-astrocytes and primary human fetal astrocytes (87.0% and 90.3%, respectively) (Figure 2D). Functional enrichment analyses (using MSigDB) demonstrated that signals regulating neuronal maturation, such as synapse or ion channel formation, were downregulated in hiPSC-astrocytes and primary human fetal astrocytes, whereas signals promoting extracellular cell adhesion and interaction were upregulated (Figure 2E). When we specifically considered just the top 100 most varying genes distinguishing hiPSC-astrocytes from hiPSC-derived NPCs and neurons, functional enrichment analysis identified a group of 19 genes related to reactivity, cytokine, interferon, T cell receptor (TCR), and antigen-processing signaling that were enriched in astrocytes (G2) (Figures 3A and S2C; Table 2).Table 2Annotation of the Top 100 Most Variable GenesMSigDBGroupOverlap SizeGroup SizeMSigDB
