Fig. 3: A distinct transcriptional profile in iNet neurons with induced TDP-43 pathology.
From: A model of human neural networks reveals NPTX2 pathology in ALS and FTLD
a, Immunofluorescence of TDP-43–HA in iNet neurons (representative image from seven repeats). Scale bar, 25 µm. b, Quantification of TDP-43–HA-positive neurons over time. Data from 2 representative experiments (out of n = 7). Each data point represents a sum of all TDP-43–HA+ cells counted from 182 fields of view of an independent well and normalized with DAPI. Each colour represents an independent experiment. Between 3,728 and 8,248 cells were analysed per data point. One-way ANOVA followed by Tukey’s multiple comparison (mean of each dataset compared with the mean of every other dataset). Data shown are mean ± s.d. OFF versus ON 1 week, P < 0.0001; OFF versus ON 2 weeks, P < 0.0001; OFF versus ON 4 weeks, P = 0.0001; ON 1 week versus ON 2 weeks, P = 0.0081; ON 1 week versus ON 4 weeks, P < 0.0001. Wk, week. c, Western blots of SarkoSpin supernatants (top) and pellets (bottom). The dashed line separates independent experiments (the experiment was repeated two times in this setting). CTF, C-terminal fragment; FL, full-length. d, UMAP of scRNA-seq TDP-43 overexpression experiment. Colours indicate clusters and dashed lines highlight different cell types. The red dashed line outlines cluster 12, which contains cells that express TDP-43–HA. e, UMAP highlighting that TDP-43–HA expression is confined to cluster 12. f,g, Dot plot with the scaled average expression of the top 10 upregulated (f) and downregulated marker genes as well as two known TDP-43 targets (g) in cluster 12 compared with other neuronal clusters.
