A transcriptomic atlas of astrocyte heterogeneity across space and time in mouse and marmoset

How astrocyte regionalization unfolds over development is not fully understood. We used single-nucleus RNA sequencing to characterize the molecular diversity of brain cells across six developmental stages and four brain regions in the mouse and marmoset brain. Our analysis revealed striking regional heterogeneity among astrocytes, particularly between telencephalic and diencephalic regions in both species. Most of the region patterning was private to astrocytes and not shared with neurons or other glial types. Though astrocytes were already regionally patterned in late embryonic stages, this region-specific astrocyte gene expression signature changed significantly over postnatal development, and its composition suggests that regional astrocytes further specialize postnatally to support their local neuronal circuits. Across mouse and marmoset, we found hundreds of species differentially expressed genes and divergence in the expression of astrocytic region- and age-differentially expressed genes. Finally, we used expansion microscopy to show that astrocyte morphology is also regionally specialized. We used 10x Genomics Chromium v3 single-nucleus RNA sequencing to characterize the molecular diversity of brain cells across six developmental stages (from late fetal to aged adult) and four brain regions (prefrontal cortex, motor cortex, striatum, and thalamus) in the mouse and marmoset brain. Each developmental time point and region combination (except for aged mouse) has 2-3 biological replicate donors. Nuclei are NOT enriched (e.g., FACS sorted) for any particular population and contain neurons, glia, and vasculature populations.