Fig. 5: ARX safeguards IN identity by repressing LMO1.

a, UMAP of integrated human and rhesus macaque IN subtypes identified in the lineage-resolved 2D screen. b, Left, dotplot showing marker gene expression in each IN subtype; right, barplot of cell numbers. Dot size denotes the expressing-cell fraction and colour denotes mean expression. c, Stacked barplots showing distributions of IN subtypes across TF perturbations in human (top) and macaque (middle) 2D culture and in human slice culture (bottom). d, UMAPs showing results of differential abundance testing in IN subtypes in ARX KD in human (top) and macaque (bottom). Left, UMAP of downsampled NT and perturbed cells from day 7, coloured by perturbation condition; right, neighbourhood graph of differential abundance testing coloured by log₂FC (FDR = 0.05). e, Heatmaps showing log₂FC in top DEGs in the IN_LMO1/RIC3 cluster versus other IN subtypes in human (left) and macaque (right). Asterisks indicate Benjamini–Hochberg (BH)-adjusted P values identified from DEseq2. f, Schematics illustrating gene expression regulation under NT, ARX KD and ARX, LMO1 dKD. g, UMAPs showing results of differential abundance testing in IN subtypes in NT, ARX KD and dKD. Left, UMAP of downsampled NT and perturbed cells coloured by conditions. Right, neighbourhood graph of differential abundance testing coloured by log₂FC (FDR = 0.05) for each contrast: ARX KD versus NT, dKD versus ARX KD and dKD versus NT. h, Beeswarm plots showing differential abundance in neighbourhoods identified in g across IN subtypes, with significant changes coloured by log₂FC. i, Dotplot showing the IN_LMO1/RIC3 marker expression in ARX, LMO1 dKD. j, Graphical summary of findings: human cortical RG gives rise sequentially to EN, IN and oligodendrocytes along developmental stages. NR2E1 KD promotes the RG lineage progression, whereas ARX KD delays the transition and impairs normal IN subtype specification. ZNF219 KD promotes differentiation of both EN and IN with an overall preference to EN. *P < 0.05; **P < 0.01; ***P < 0.001. Illustrations in c–e and schematic in f created in BioRender. Nowakowski, T. (https://BioRender.com/7cr6o12). Illustration in j created by H. Pinheiro (www.hpinheiro.com).