Fig. 3. Consistent dysregulation of presynaptic and CASK-interacting genes in bulk RNA sequencing after 28 days of differentiation.
a Upregulated and b downregulated gene sets emerging from GSEA in bulk RNA-sequencing data from mutation carriers compared with controls. c GSEA for CASK-interacting proteins (CASK PPI), ASD risk genes (SFARI), and NDD genes (NDD) in bulk RNA-sequencing data from mutation carriers compared with controls. d Network of CASK-interacting proteins with upregulation marked in blue and downregulation in red. e Venn diagram illustrating the top upregulated and downregulated genes in ASDCASK_SS and MICPCHCASK_dup4/5 in comparison with sex-matched controls. f Representative confocal microscopy images of neurons differentiated for 28 days and immunostained for Synapsin-1/2 (green), Homer-1 (red), and Hoechst (blue). Scale = 10 µm. g Quantification of Homer-1 and h Synapsin-1/2 particle size (n = 4 per cell line). Statistical differences between cell lines were calculated using ANOVA with post hoc Tukey HSD. *p < 0.05, **p < 0.01, ***p < 0.001. Asterisks are color-coded according to case cell lines.