Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

Cell-type specific developmental defects inPTEN-mutant cortical organoids converge on abnormal circuit activity

“…1i-j and Supplementary Fig. 2d-e ), when the highest diversity of progenitor and projection neuron subtypes is found in these organoids (Velasco et al, 2019, Uzquiano et al, Cell, 2022). In both genetic backgrounds, heterozygous PTEN organoids showed a consistent significant increase in oRG (FDR<0.05, logistic mixed models; Fig.…”

“…Because PTEN and its downstream effectors AKT and MAPK1 are ubiquitously expressed across all cortical cell types during control organoid development by single-cell RNA-seq (scRNA-seq) ( Supplementary Fig. 1f ) (Uzquiano et al, Cell, 2022), we investigated the celltype-specific phenotypes caused by heterozygous mutation in PTEN , using scRNA-seq of individual organoids at one month in culture ( Fig. 1a-b and Supplementary Fig.…”

“…PTEN loss of function in early mouse development has been reported to affect the spatial organization of the mouse brain (Groszer et al, Science, 2001; Li et al, J Cell Biochem, 2003). We therefore investigated the effects of a heterozygous mutation in PTEN on spatial organization of organoid cell types at two months of culture, when this brain organoid model shows clear structural organization of progenitors into rosettes around the organoid periphery (Uzquiano et al, Cell, 2022), using spatial transcriptomics with Slide-seq on heterozygous and isogenic control Mito210 organoids. The spatial organization for most cell types was similar between conditions ( Supplementary Fig.…”

“…We first calculated the differentially expressed genes (DEG) for each cell type between control and heterozygous mutant PTEN organoids at each time point (see Methods). We then used an existing high-resolution developmental atlas of human cortical organoids we previously obtained with the same differentiation protocol (Velasco et al, 2019, Uzquiano et al, Cell, 2022) to define gene changes associated with developmental time in each cell type. We calculated the genes that change over time in individual cell types across cortical organoid development, from all of the cell lines in that dataset, including the two used here (Mito210 and PGP1), as well as two others used previously (HUES66 and GM08330), depending on time point.…”

“…e) Spearman correlation of DEGs between each cortical cell type within control and PTEN heterozygous mutant organoids at three months, and genes that change within that cell type from two months to four months in control organoids (Uzquiano et al, bioRxiv, 2022). Correlation is calculated on each gene’s signed logFC.…”