Fig. 4: Cross-comparisons among FUS-, TARDBP-, and C9orf72-ALS reveal shared dysfunctions that converge on metabolic pathways.

a Strategy to uncover shared dysfunction across familial ALS forms that could uncover convergent pathomechanisms that are intrinsic to motor neurons. Cross-comparison of FUS-ALS and TARDBP-ALS motor neurons across our single-cell RNA-Seq data set (b–d) followed by cross-comparison with external bulk RNA-Seq dataset from C9orf72-ALS³³ was thus conducted (e, f). b Venn diagram showing overlap of DEGs between all FUS mutant motor neurons, as well as the TARDBP mutant motor neurons, as compared to control. Genes with an adjusted p-value of <0.05 were considered differentially expressed. c, Venn diagram showing overlap in dysregulated biological processes between FUS LOF lines (all FUS lines), FUS GOF lines (excluding the FUS KO), and the TDP-43 M337V line following GSEA. For b, c in each compartment, the top number represents upregulated genes/pathways, while the bottom number represents downregulated genes/pathways. Pathways with an adjusted p-value of <0.05 (two-sided DEA with DESeq2 corrected for an FDR of 0.05) were considered significantly up- or downregulated. d Heatmaps displaying normalized enrichment scores from GSEA of selected groups of pathways from the Venn diagram in (c). Motor neurons are compared to V2a interneurons to show specific or stronger regulation of these pathways in motor neurons. e Venn diagram depicting the overlap between dysregulated biological processes in TARDBP M337V and the ALS-FUS GOF and LOF groups defined in Fig. 3. f Venn diagram depicting the overlap between dysregulated pathways from the single cells RNA-Seq of ALS mutant motor neurons (FUS R495X, FUS P525L lines and TARDBP M337V) and the bulk RNA-Seq of C9orf72-ALS motor neurons. g Pairwise set comparisons of the dysregulated pathways in the Venn diagram from (f). The odds ratio of the overlap against all dysregulated pathways in the Venn diagram is shown as the bubble colour. The bubble size is the adjusted p-value of the overlap calculated by two-sided Fisher’s exact test; the asterisk indicates comparisons for which the odds ratio is larger than five-fold.