TDP-43 loss induces cryptic polyadenylation in ALS/FTD

Area of Science:

• Neuroscience
• Molecular Biology
• Genetics

Background:

• Nuclear TDP-43 depletion and cytoplasmic aggregation are hallmarks of ALS.
• TDP-43 loss is known to cause cryptic exon de-repression.
• Cryptic alternative polyadenylation (APA) events induced by TDP-43 loss have been understudied.

Purpose of the Study:

• To develop a bioinformatic pipeline for identifying cryptic APA events.
• To investigate cryptic APA in induced pluripotent stem cell (iPSC)-derived neurons with TDP-43 loss.
• To analyze the occurrence of cryptic APA in postmortem brain tissue from ALS and frontotemporal dementia (FTD) patients.

Main Methods:

• Bioinformatic pipeline for identifying alternative last exons, 3'UTR extensions, and intronic polyadenylation APA.
• RNA sequencing (RNA-seq), SLAM-seq, and ribosome profiling (Ribo-seq) on iPSC-derived neurons.
• Analysis of TDP-43 binding sites enrichment at cryptic APA sites.

Main Results:

• Identified cryptic APA events, including alternative last exons, 3'UTR extensions, and intronic polyadenylation, in iPSC-derived neurons lacking TDP-43.
• TDP-43 binding sites were enriched at these cryptic APA sites, with TDP-43 showing both repressive and enhancing roles in APA.
• All categories of cryptic APA were also found in postmortem brain tissue from ALS and FTD patients.
• Distinct cryptic APA categories differentially affect transcript levels, RNA stability, and translation, with 3'UTR extensions increasing RNA stability and translation.

Conclusions:

• TDP-43 nuclear depletion induces a range of cryptic APA events.
• These cryptic APA events have significant downstream effects on RNA regulation and protein production.
• The findings expand the known molecular consequences of TDP-43 dysfunction in ALS and FTD.