Brain regional identity and cell type specificity landscape of human cortical organoid models

ABSTRACT In vitro models of corticogenesis using mouse and human pluripotent stem cells (PSC) have greatly improved our understanding of human brain development and disease. Among these, 3D cortical organoid systems are able to recapitulate some aspects of in vivo cytoarchitecture of the developing cortex. Here, we tested three cortical organoid protocols for brain regional identity, cell type-specificity and neuronal maturation. Overall all protocols gave rise to organoids that displayed a time-dependent expression of neuronal maturation genes such as those involved in the establishment of synapses and neuronal function. We showed that three months old cortical organoids showed a pattern of gene expression that resembled late human embryonic cortex. Comparatively, directed differentiation methods without WNT activation gave rise to the highest degree of cortical regional identity in brain organoids. Whereas, default “intrinsic” brain organoid differentiation produced the broadest range of cell types such as neurons, astrocytes and hematopoietic-lineage derived microglia cells of the brain. These results suggest that cortical organoid models produce diverse outcomes in terms of brain regional identity and cell type specificity and emphasize the importance of selecting the correct model for the right application.