Extended Data Fig. 9: Spatial, temporal, and molecular distinctions among initial LGE-derived neurons.
From: The development and evolution of inhibitory neurons in primate cerebrum
a. Bar plot of the proportion of cells from each initial class across cortical regions for CGE-, LGE- and MGE-derived classes highlights frontal lobe enrichment of LGE classes during sampling. b. Schematic for c, showing cartoon scatter plots for the expression of two genes in individual cells regressed against latent time (left) to describe genes that activate or inactivate during neuronal differentiation, followed by Venn diagrams showing the overlap of dynamically regulated genes between pairs of initial classes used to calculate Jaccard indices. c. Heatmap of Jaccard indices of significantly overlapping lists of dynamic genes between cell classes of Holm-Å Ãdák corrected linear regression q value < 0.05 on scaled and normalized gene expression to address the extent of shared versus cell type-specific trajectories during post-mitotic differentiation of initial classes. Bar graphs on axes represent the total number of significant genes activating/inactivating. Direct and indirect medium spiny neurons (LGE_FOXP1/ISL1 and LGE_FOXP1/PENK) show strong overlap of both activating and inactivating genes, despite early partitioning as distinct initial classes, while presumed eccentric spiny neurons from LGE_FOXP2/TSHZ1 show strong overlap of activating genes (see also g) but not inactivating genes. Conversely, MGE_CRABP1/MAF and MGE_CRABP1/TAC3 classes show strong overlap of inactivating genes among a smaller overall set of dynamically regulated genes, but little overlap in activating genes. d. Heatmap of selected marker expression of LGE-derived striatal initial and terminal classes, scaled by gene. e. Gene expression of dynamic dLGE marker genes in macaque LGE_FOXP2/TSHZ1 cells across shared latent time, ordered by latent time value and divided into 10 equally sized bins to provide stable mean expression values. f. Gene expression of dynamic marker genes in macaque cells across shared latent time, grouped by initial class, ordered by latent time value and divided into 30 equally sized bins to provide stable mean expression values. g. Venn diagram of intersections of significantly activating gene sets in LGE initial classes. In contrast to LGE_MEIS2/PAX6, the LGE_FOXP2/TSHZ1 class activates a large set of shared SPN genes during neuronal differentiation as inferred by latent time trajectories.
