Chemogenetic activation of astrocytes in the hippocampus and cortex changes the transcriptome of microglia

Astrocytes are the most common glial cell type in the brain, yet, it is still not clear how their activation affects the transcriptome of neighboring microglia and neurons. Engineered G protein-coupled receptors (GPCRs) called Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) make it possible to selectively activate specific cell types, such as neurons and astrocytes. By combining the selective activation of astrocytes with single cell RNA sequencing, we were able to study transcriptional changes that occur in response to the activation of astrocytes at the single cell level. Interestingly, our data shows that long-term activation of astrocytes in healthy mice results in dramatic alteration in the transcriptome of astrocytes and microglia. Genes that were differentially expressed in these Gq-DREADD-activated astrocytes were involved in neurogenesis and low-density lipoprotein particle biology, while those in the microglia were involved in lipoprotein handling, purinergic receptor activity, and immune cell migration and chemotaxis. Furthermore, network analysis showed that Gq-DREADD-mediated activation in astrocytes resulted in an upregulation of genes involved in the GPCR signaling pathways and calcium ion homeostasis, confirming astrocyte activation through Gq-DREADD expression. Our findings show the importance of considering transcriptomic alterations in microglia after the activation of astrocytes in in vivo models. Therefore, our data will serve as a resource for the broader neuroscience community. Overall design: Single cells were isolated from the hippocampus and cortex of C57BL/6J mice using ice-cold accutase. Myelin was removed using the Myltenyi's Myelin Depletion Protocol and droplet-based single cell RNA sequencing was performed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2. Libraries were sequenced on an Illumina NovaSeq 6000 SP.