TDP-43 dysregulation of polyadenylation site selection is a defining feature of RNA misprocessing in amyotrophic lateral sclerosis and frontotemporal dementia
Frederick J. Arnold, … , Wei Li, Albert R. La Spada
Frederick J. Arnold, … , Wei Li, Albert R. La Spada
Published June 2, 2025
Citation Information: J Clin Invest. 2025;135(11):e182088. https://doi.org/10.1172/JCI182088.
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Research Article Genetics Neuroscience

TDP-43 dysregulation of polyadenylation site selection is a defining feature of RNA misprocessing in amyotrophic lateral sclerosis and frontotemporal dementia

Abstract

Nuclear clearance and cytoplasmic aggregation of TAR DNA-binding protein 43 (TDP-43) are observed in many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although TDP-43 dysregulation of splicing has emerged as a key event in these diseases, TDP-43 can also regulate polyadenylation; yet this has not been adequately studied. Here, we applied the dynamic analysis of polyadenylation from an RNA-Seq (DaPars) tool to ALS/FTD transcriptome datasets and report extensive alternative polyadenylation (APA) upon TDP-43 alteration in ALS/FTD cell models and postmortem ALS/FTD neuronal nuclei. Importantly, many identified APA genes highlight pathways implicated in ALS/FTD pathogenesis. To determine the functional relevance of APA elicited by TDP-43 nuclear depletion, we examined microtubule affinity regulating kinase 3 (MARK3). Nuclear loss of TDP-43 yielded increased expression of MARK3 transcripts with longer 3′ UTRs, corresponding with a change in the subcellular distribution of MARK3 and increased neuronal tau S262 phosphorylation. Our findings define changes in polyadenylation site selection as a previously understudied feature of TDP-43–driven disease pathology in ALS/FTD and highlight a potentially important mechanistic link between TDP-43 dysfunction and tau regulation.

Authors

Frederick J. Arnold, Ya Cui, Sebastian Michels, Michael R. Colwin, Cameron M. Stockford, Wenbin Ye, Vidhya Maheswari Jawahar, Karen Jansen-West, Julien Philippe, Ravinder Gulia, Yunzi Gou, Oliver H. Tam, Sneha Menon, Wendy G. Situ, Saira L. Cazarez, Aryan Zandi, Kean C.K. Ehsani, Sierra Howard, Dennis W. Dickson, Molly Gale Hammell, Mercedes Prudencio, Leonard Petrucelli, Wei Li, Albert R. La Spada

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Figure 6

Nuclear clearance of TDP-43 induces APA in ALS/FTD patient neurons.

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Nuclear clearance of TDP-43 induces APA in ALS/FTD patient neurons. (A) ...
(A) Volcano plot depicting APA genes in neuronal nuclei from 7 postmortem ALS/FTD neocortex samples sorted by FACS for the presence or absence of nuclear TDP-43. APA genes with P < 0.05 and ΔPDUI ≤ –0.1 are depicted in blue and APA genes with P < 0.05 and ΔPDUI ≥ 0.1 are in red. (B) eCLIP-Seq data showing the location of TDP-43 binding within the MARK3 3′ UTR, as well as in an upstream intronic region (green). MARK3 binding within the 3′ UTR is immediately upstream of the distal shift in 3′ UTR usage observed in TDP-43 negative neurons (blue versus red RNA-Seq tracks). (C) RT-PCR analysis and qRT-PCR quantification of MARK3 APA in SH-SY5Y cells transfected with minigene constructs in which the MARK3 3′ UTR was cloned downstream of the NanoLuc luciferase gene with WT sequence or with the TDP-43 binding motif deleted (Del). *P < 0.05; unpaired 2-tailed t test. n = 4 biological replicates. (D) RT-PCR of distal 3′ UTR (top band) and proximal 3′ UTR (bottom band) of MARK3 in iPSC-MNs in which TDP-43 was knocked down with shRNA for 10 days. *P < 0.05; unpaired 2-tailed t test. n = 3 biological replicates. All data are represented as mean values ± SEM.