DECIPHERING THE IMPACT OF TDP-43 LOSS-OF-FUNCTION ON ALTERNATIVE POLYADENYLATION IN THE ALS-FTD SPECTRUM

Ageing-associated neurodegeneration is linked to the dysregulation of RNA-binding proteins and post-transcriptional processing, with TDP-43 proteinopathy serving as a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). While TDP-43 is a recognized master regulator of alternative splicing, its role in modulating alternative polyadenylation (APA) is critical to understanding neuronal dysfunction. This study characterizes APA events following nuclear TDP-43 depletion in SH-SY5Y knockdown models and iPSC-derived motor neurons using 3′ end RNA-seq to to identify changes in polyadenylation, and analyze proximal versus distal polyA site usage. Our results corroborate widespread APA changes, including some previously described in STMN2, SMC1A and G3BP1 (also validated by our in-house targeted 3´end RNA-Seq protocol), as well as new transcripts directly related to neuronal dysfunction in the ALS-FTD spectrum. Most of the polyA sites that we identified were in 3´UTRs, which are usually repressed by TDP-43 when it is functional. The lengthened of these sites is also associated with a change in RNA levels of at least 1.5-fold, which suggests that APA changes could also affect not only gene expression but also protein levels. Together, these findings provide evidence of the crucial role of APA in maintaining neuronal health, as well as a catalogue of candidate RNA isoforms associated with TDP-43 pathology that we will use in further studies to design antisense RNA strategies that correct the most relevant misprocessing events linked to the ALS-FTD spectrum.