Hypoxia dysregulates circadian rhythm and causes synapse elimination defects in astrocytes

In this study, we used human cortical organoids (hCOs) derived from induced pluripotent stem cells (iPSCs) to examine how hypoxia exposure interferes with astrocyte synapse engulfment at 6 months in culture and 10 months in culture, equivalent to mid fetal- or neonatal-equivalent stages of development, respectively. We identified that hypoxia inhibits the synaptosome engulfment by human astrocytes at both developmental stages, with a more pronounced phenotype in 10 months astrocytes. Transcriptional analyses revealed disruptions in circadian rhythm pathways in hypoxic astrocytes, but not neurons, and PER2 luciferase assays (PER2::LUC) validated the presence of circadian rhythms and their disruption by hypoxia in intact hCOs, with more pronounced rhythms in 10 months hCOs. We performed differential gene expression and Gene Ontology analysis using bulk RNA-seq of day 200 and day 300 human cortical organoid exposed to control or hypoxic conditions.