Fig. 3: PACS1^(+/R203W) mature glutamatergic neurons have impaired expression of transcripts involved in ion transport and synaptic signaling.

a Dot plot showing the number of differentially expressed genes (DEGs) identified in each cell group at the two time points. Size indicates the number of DEGs while color indicates direction of change. b A volcano plot showing select top DEGs. Color indicates cell type and size correlates to a combined metric of log₂FC and p_adj. All 277 DEGs are shown in Fig. S9, Data S1, and the Source Data file. y axis is shown on a log₁₀ scale with a cutoff of p_adj < 0.05 for both DEG identification methods used. c–e Nested pie chart showing root and branch significant gene ontology enrichments with the colored dots above indicating which cell types were included in the analysis and width of the pie correlating to -log(p) of the GO term. Statistics were calculated using the Fisher’s Exact test with correction facilitated within the elim algorithm (see Methods). GO terms for DEGs up and downregulated across all PACS1^(+/R203W) cell types are shown in (c); GO terms for DEGs upregulated in PACS1^(+/R203W) immature neurons are shown in (d); and the GO terms for DEGs upregulated in PACS1^(+/R203W) mature neuron groups are shown in (e). f Functional enrichment and pathway analysis results of PACS1^(+/R203W) DEGs in the mature glutamatergic neuron groups generated with IPA analysis. Gene color indicates fold change with green being downregulated and red upregulated in PACS1^(+/R203W) models. Orange indicates IPA predicts activation of the pathway, and blue repression. p_adj = 0.0035 for neurotransmission, p_adj = 0.019 for dendritic growth/branching, and p_adj = 0.016 for GABA receptor signaling using a right-tailed Fisher’s Exact test with a Benjamini-Hochberg correction for multiple testing. The GABA receptor signaling term refers to analysis of upregulated genes while the other terms include both up and downregulated genes. g Feature plots of top PACS1^(+/R203W) DEGs implicated in IPA analysis. Cells have been down-sampled so the same number is shown for each genotype. Data is shown from two C2, one CRISPR R203W, and one A1 day 88 organoid from one independent differentiation. Plots for each sample are in Fig. S12. Scale is in units of log₁₀(value + 0.1).