TDP-43 Cooperates With Nuclear Exosome Targeting Complex in Regulating SCARNA2 Metabolism
Yuki Oshima1, Hidefumi Suzuki2, Ryota Abe3, Shintaro Ogawa2, Yoko Ike2, Hiroaki Yaguchi1, Hidehisa Takahashi2, Ichiro Yabe1
1Department of Neurology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, 2Department of Molecular Biology, Yokohama City University, 3Department of Neurology and Stroke Medicine, Yokohama City University
Objective:

To elucidate the intracellular molecular mechanism of TAR DNA-binding protein of 43 kDa（TDP-43）and its role in the pathogenesis of amyotrophic lateral sclerosis (ALS).

Background:

TDP-43 has been implicated in diverse aspects of RNA metabolism, including transcriptional regulation, mRNA transport and degradation. Recently, it has been shown that TDP-43 is involved in regulation of non-coding RNA (ncRNA) metabolism. Nevertheless, the molecular details of how TDP-43 contributes to RNA surveillance remain unclear. We performed several omics analysis to address the molecular mechanism of TDP-43 in regulation of ncRNA metabolism.

Design/Methods:

To identify RNAs bound to TDP-43, we performed ultraviolet RNA immunoprecipitation (UV-RIP) followed by RNA-seq using doxycycline-inducible FLAG-TDP-43 TREx293 cells. To identify TDP-43-associated proteins, we conducted immunoprecipitation–mass spectrometry analysis under the same conditions. To investigate functional consequences, we established TDP-43-FKBP12F36V knock-in cells using the dTAG system to induce rapid protein degradation, followed by RNA-seq analysis. In addition, single and double knockdowns of TDP-43 and NEXT components were performed, and RNA levels were measured by RT-qPCR. We used ChatGPT (GPT-5; OpenAI) to assist with R code for figure preparation. Analyses and data interpretation were conducted by the authors.

Results:
UV-RIP-Seq revealed SCARNA2 as RNA bound by TDP-43. Proteomic analysis identified NEXT complex as TDP-43 interacting factor. dTAG-mediated TDP-43 degradation or knockdown of the component of NEXT complex, RBM7 increased SCARNA2 levels, while further increase of SCARNA2 was not observed under simultaneous depletion of TDP-43 and RBM7. These results indicate that TDP-43 and NEXT complex cooperatively function in the same pathway to regulate the degradation of SCARNA2.
Conclusions:
Our findings demonstrate that TDP-43 cooperates with the NEXT complex to mediate the degradation of SCARNA2. This work uncovers a novel molecular mechanism of RNA surveillance and provides new insight into how dysregulation of TDP-43 may contribute to the pathogenesis of ALS.
10.1212/WNL.0000000000215338
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