Effects of overexpression of a C9orf72 repeat expansion linked to GFP, or a GFP control in human HEK293 cells, in the presence or absence of the EIF2B activator DNL343.

Neuronal TDP-43 aggregates are a hallmark ALS pathology. The integrated stress response (ISR) occurs downstream of TDP-43 pathology and may exacerbate TDP-43 aggregation and neurodegeneration. Here we assessed the effects of overexpression of a GFP-taggted C9orf72 repeat expansion in HEK293 cells on the transcriptome, in the presence or ascence of the EIF2B activiting small molecule DNL343. Expression of (G4C2)71-GFP upregulated most of the pre-defined ISR genes compared to GFP expression alone. These transcriptional changes were largely corrected by DNL343 treatment. HEK293 cells were engineered to overexpress either GFP-taggted C9orf72 repeat expansion (e.g.(G4C2)71-GFP) or GFP alone. After inducing protein expression for24 hours, cells were treated with either DMSO or 1 uM DNL343 for 2.5 hours before harvesting total RNA. The experiment was performed in 6 replicates, e.g. cells were treated independently on 6 different days. One sample failed quality control, leaving 23 samples in total for 3-tag RNA-sequencing to quantify transcriptome-wide gene expression levels.