Fig. 6
Widespread transcriptional changes in rNLS8 mice are modestly rescued by immunization targeting the glycine-rich region. A Differentially expressed genes from rNLS8 mice (TDP-PBS, TDP10 + 12, TDP15) compared to controls (ctrl PBS) and motor cortex (MCtx) and spinal cord (SC) of sporadic ALS patients compared to no-disease controls (dataset from [25]). From each group the 25 genes with largest absolute log2 fold change (LFC) also reaching statistical significance (indicated by asterisk) are depicted. Color code denotes LFC. B Principal component analysis (PCA) of transcriptomes separates animals based on genotype (control vs. rNLS8), but not on therapeutic intervention or gender. C Gene ontology analysis of differentially expressed genes (cutoff |LFC|> 1) in ALS spinal cord and TDP-PBS mice, each both compared to non-diseased controls. Manual selection of categories with > 4 genes. Full list is shown in Additional file 3: Table S2. D Fold-change of genes differentially expressed in TDP-PBS vs. control mice plotted against the fold-change between vaccinated and PBS-treated rNLS8 animals. Blue line shows linear regression. Pearson's product-moment correlation shows partial rescue of gene expression (p < 2*10–16 for both, correlation coefficient −0.49 and −0.12 as indicated). E Cytokine levels determined by multiplex assay from cortical tissue show inflammatory response in rNLS8 animals. Pairwise t-test with Benjamini–Hochberg correction revealed statistically significant differences between ctrl (monogenic) and bigenic TDP-PBS animals: IL-1β: ctrl PBS p = 2.57*10–5, ctrl VAX p = 0.004; IP-10: ctrl PBS p = 6.26*10–5, ctrl VAX: p = 6.26*10–5; KC/GRO: ctrl PBS p = 9.17*10–4, ctrl VAX p = 2.13*10–4; MCP-1: ctrl PBS p = 7.98*10–6, ctrl VAX p = 7.98*10–6; MIP-1α: ctrl PBS p = 3.44*10–5, ctrl VAX p = 3.44*10–5; TNF-α: ctrl PBS p = 5.64*10–4, ctrl VAX p = 5.64*10–4. TNF-α and IL-1β: Control (ctrl) PBS n = 6, ctrl VAX n = 6, TDP-PBS n = 10, TDP5 + 7 n = 6, TDP8 + 9 n = 9, TDP10 + 12 n = 9, and TDP15 n = 7; IP-10, KC/GRO, MCP-1 and MIP-1α: Control (ctrl) PBS n = 10, ctrl VAX n = 10, TDP-PBS n = 10, TDP5 + 7 n = 13, TDP8 + 9 n = 12, TDP10 + 12 n = 12, and TDP15 n = 12. Non-affected cytokines are shown in Supplemental Fig. S4C