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 3

CNPY3 APA increases the expression of an isoform variant with an alternative last exon in neuronal cells and in ALS/FTD and FTLD-TDP patient tissue.

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CNPY3 APA increases the expression of an isoform variant with an altern...
(A) RT-PCR analysis and qRT-PCR quantification of CNPY3 APA isoforms with or without TDP-43 knockdown in SH-SY5Y cells. **P < 0.01; unpaired 2-tailed t test. n = 3 biological replicates. (B) RT-PCR analysis and qRT-PCR quantification of CNPY3 APA isoforms in SH-SY5Y cells transfected with minigene constructs encoding exon 3, intron 3, and exon 4 of the CNPY3 gene (NM_006586.5) with WT sequence or with the TDP-43–binding motif deleted (Del). *P < 0.05; unpaired 2-tailed t test. n = 4 biological replicates. (C) RT-PCR analysis and qRT-PCR quantification of CNPY3 APA isoforms with or without TDP-43 knockdown in i3Neurons. **P < 0.01; unpaired 2-tailed t test. n = 3 biological replicates. (D) Immunoblot analysis of CNPY3 in i3Neurons reveals that CNPY3 APA corresponds with a decrease in CNPY3 protein levels. *P < 0.05; unpaired 2-tailed t test. n = 3 biological replicates. (E) qRT-PCR quantification of CNPY3 APA isoforms in postmortem frontal cortex from healthy controls versus FTLD-TDP or ALS/FTD patients with confirmed CE inclusion in UNC13A. **P < 0.01; unpaired 2-tailed t test. n = 11 (control), n = 30 (UNC13A CE). All data are represented as mean values ± SEM.