Figure 2.

Interactions of FUS and TDP-43 are affected by DNA damage. (A) AE-MS was performed on HeLa-Kyoto cells stably expressing LAP-tagged TDP-43 or FUS and treated with either DMSO or 5 μM etoposide for 1 h. After enrichment with anti-GFP camelid antibodies, interactors were digested in solution for LC–MS/MS. LFQ analysis was used to determine enrichment above GFP or LAP-SARS control proteins (p < 0.05, Student’s t-test; N = 4 for each treatment and control). (B) Stable LAP-FUS (left) or LAP-TDP43 (right) cell lines were found by western analysis to express the tagged proteins below the endogenous levels and neither the tagged nor endogenous protein levels were affected by 1 h of etoposide treatment. (C) Heat maps show changes to interactions shared by both TDP-43 and FUS (left, N = 316), FUS only (center, N = 289), or TDP-43 only (right, N = 139). Fold changes are shown as increases (green) or decreases (red). Blue bars to the right of each heat map indicate significant changes (p ≤ 0.05, Student’s t-test). The Venn diagram summarizes the number of interactors shared by TDP-43 or FUS or unique to those enrichments. (D) Complex network analysis was performed for interactors with either TDP-43 (left, red) or FUS (blue, right). The log₁₀ of the p-value for the significance of enrichment is plotted for each GO term. A list of interactors for each GO term can be found in Table 1.