Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids

Microglia are resident macrophages in the brain that emerge in early development and respond to the local environment by altering their molecular and phenotypic states. Fundamental questions about microglia diversity and function during development remain unanswered because we lack experimental strategies to interrogate their interactions with other cell types and responses to perturbations ex vivo. We compared human microglia states across culture models, including cultured primary and pluripotent stem cell-derived microglia. We developed a report card of gene expression signatures across these distinct models to facilitate characterization of their responses across experimental models, perturbations, and disease conditions. Xenotransplantation of human microglia into cerebral organoids allowed us to characterize key transcriptional programs of developing microglia in vitro and reveal that microglia induce transcriptional changes in neural stem cells and decrease interferon signaling response genes. Microglia additionally accelerate the emergence of synchronized oscillatory network activity in brain organoids by modulating synaptic density.

Automated summary

The study compared human microglia states across different culture models and developed a report card of gene expression signatures to facilitate characterization of their responses under various conditions. Xenotransplantation of human microglia into cerebral organoids allowed the characterization of key transcriptional programs of developing microglia and their effects on neural stem cells. Additionally, microglia were found to modulate synaptic density and accelerate synchronized oscillatory network activity in brain organoids.