Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

Abstract

Direct comparisons of human and non-human primate brain tissue have the potential to reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is largely inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. First, we systematically evaluated the fidelity of organoid models to primary human and macaque cortex, finding organoid models preserve gene regulatory networks related to cell types and developmental processes but exhibit increased metabolic stress. Second, we identified 261 genes differentially expressed in human compared to chimpanzee organoids and macaque cortex. Many of these genes overlap with human-specific segmental duplications and a subset suggest increased PI3K/AKT/mTOR activation in human outer radial glia. Together, our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.

A critical look: Challenges in differentiating human pluripotent stem cells into desired cell types and organoids

“…Such scRNAseq analyses have revealed substantial variation between individual experiments and among organoids from the same experiment (Quadrato et al, 2017) or amongst organoids derived from different hPSC lines (Pollen et al, 2019), although other analyses suggested less variability (Velasco et al, 2019;Yoon et al, 2019). In any case, the presence of mesenchymal-like cells that express MYOSIN, COLLAGEN, and DECORIN genes (Camp et al, 2015;Pollen et al, 2019;Quadrato et al, 2017) in current-generation brain organoids is unexpected (Figure 6c). It remains to be determined whether these mesenchymal cells foster, or might occlude, proper brain development and the spatial organization of such organoids.…”

“…Indeed, scRNAseq recently revealed that while hPSCderived substantia nigra dopaminergic neurons approximated their in vivo fetal counterparts, they also shared certain attributes with other mutually exclusive lineages (La Manno et al, 2016). Expanding this scRNAseq analysis to additional hPSC-derived neural lineages revealed that in vitro-derived cell types consistently displayed a perturbed metabolic signature entailing elevated glycolysis and an unfolded protein response by comparison to primary human fetal cell types (Pollen et al, 2019).…”

“…It is possible to obtain cells from mid-to late-gestation human embryos or from adult humans as comparators for terminally differentiated cell types from hPSCs. For instance, scRNAseq and other transcriptional assays have been used to directly compare neural cells isolated from a human fetus against their hPSC-derived counterparts (Kirkeby et al, 2012;La Manno et al, 2016;Pollen et al, 2019) (Figure 5d).…”

“…Finally, while cellular heterogeneity is integral to the very definition of organoids, excessive or unwanted heterogeneity may be deleterious. By way of example, scRNAseq has revealed the coexistence of dorsal forebrain, ventral forebrain, mesenchymal and other cell types in hPSC-derived brain organoids (Camp et al, 2015;Pollen et al, 2019;Quadrato et al, 2017). Such scRNAseq analyses have revealed substantial variation between individual experiments and among organoids from the same experiment (Quadrato et al, 2017) or amongst organoids derived from different hPSC lines (Pollen et al, 2019), although other analyses suggested less variability (Velasco et al, 2019;Yoon et al, 2019).…”

“…By way of example, scRNAseq has revealed the coexistence of dorsal forebrain, ventral forebrain, mesenchymal and other cell types in hPSC-derived brain organoids (Camp et al, 2015;Pollen et al, 2019;Quadrato et al, 2017). Such scRNAseq analyses have revealed substantial variation between individual experiments and among organoids from the same experiment (Quadrato et al, 2017) or amongst organoids derived from different hPSC lines (Pollen et al, 2019), although other analyses suggested less variability (Velasco et al, 2019;Yoon et al, 2019). In any case, the presence of mesenchymal-like cells that express MYOSIN, COLLAGEN, and DECORIN genes (Camp et al, 2015;Pollen et al, 2019;Quadrato et al, 2017) in current-generation brain organoids is unexpected (Figure 6c).…”