Cerebral organoids-3D cultures of human cerebral tissue derived from pluripotent stem cells-have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear.Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and previously unidentified interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single-cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.

Evolutionary expansion of the human neocortex reflects increased amplification of basal progenitors in the subventricular zone, producing more neurons during fetal corticogenesis. In this work, we analyze the transcriptomes of distinct progenitor subpopulations isolated by a cell polarity-based approach from developing mouse and human neocortex. We identify 56 genes preferentially expressed in human apical and basal radial glia that lack mouse orthologs. Among these, ARHGAP11B has the highest degree of radial glia-specific expression. ARHGAP11B arose from partial duplication of ARHGAP11A (which encodes a Rho guanosine triphosphatase-activating protein) on the human lineage after separation from the chimpanzee lineage. Expression of ARHGAP11B in embryonic mouse neocortex promotes basal progenitor generation and self-renewal and can increase cortical plate area and induce gyrification. Hence, ARHGAP11B may have contributed to evolutionary expansion of human neocortex.

The expansion of the neocortex during mammalian brain evolution results primarily from an increase in neural progenitor cell divisions in its two principal germinal zones during development, the ventricular zone (VZ) and the subventricular zone (SVZ). Using mRNA sequencing, we analyzed the transcriptomes of fetal human and embryonic mouse VZ, SVZ, and cortical plate. In mouse, the transcriptome of the SVZ was more similar to that of the cortical plate than that of the VZ, whereas in human the opposite was the case, with the inner and outer SVZ being highly related to each other despite their cytoarchitectonic differences. We describe sets of genes that are up-or down-regulated in each germinal zone. These data suggest that cell adhesion and cell-extracellular matrix interactions promote the proliferation and self-renewal of neural progenitors in the developing human neocortex. Notably, relevant extracellular matrix-associated genes include distinct sets of collagens, laminins, proteoglycans, and integrins, along with specific sets of growth factors and morphogens. Our data establish a basis for identifying novel cell-type markers and open up avenues to unravel the molecular basis of neocortex expansion during evolution.cerebral cortex | neural stem cells | neurogenesis N eocortex expansion is a hallmark of mammalian brain evolution. With regard to neuron number, a major cause of this expansion is the increase in the population size of neural stem and progenitor cells (NSPCs) and the number of divisions that each of the various NSPC types undergoes during cortical development (1-4). Two principal classes of these cells can be distinguished based on the location of their mitosis: (i) apical progenitors (APs), which undergo mitosis at the luminal surface of the ventricular zone (VZ); and (ii) basal progenitors (BPs), which undergo mitosis at an abventricular location, typically in the subventricular zone (SVZ) (2, 5, 6). Neurons born from AP and BP cell divisions migrate radially and settle at the basal (pial) side of the developing cortical wall to form the cortical plate (CP).Both APs and BPs comprise several types of NSPCs that differ in key cell biological features (e.g., cell polarity, cell processes, cell-to-cell junctions, nuclear migration) and in the principal modes of cell division (symmetric proliferative vs. asymmetric self-renewing vs. symmetric or asymmetric consumptive) (2, 5-10). APs comprise neuroepithelial cells, which transform into apical radial glial cells (aRGCs) at the onset of neurogenesis (11), and short neural precursors (12). BPs include basal (or outer) radial glial cells (bRGCs), transit amplifying progenitors (TAPs), and intermediate progenitor cells (IPCs) (2, 3, 13).The evolutionary expansion of the neocortex is associated with an increase in the thickness of the SVZ, which develops into two cytoarchitecturally distinct zones, an inner SVZ (ISVZ) and an outer SVZ (OSVZ) (1-4, 14, 15). The evolutionary increase in the SVZ is accompanied by a change in the proportion of BP subtypes. Fo...