Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes

Norah Al-Azzam; Jenny H To; Vaishali Gautam; Lena A Street; Chloe B Nguyen; Jack T Naritomi; Dylan C Lam; Assael A Madrigal; Benjamin Lee; Wenhao Jin; Anthony Avina; Orel Mizrahi; Jasmine R Mueller; Willard Ford; Cara R Schiavon; Elena Rebollo; Anthony Q Vu; Steven M Blue; Yashwin L Madakamutil; Uri Manor; Jeffrey D Rothstein; Alyssa N Coyne; Marko Jovanovic; Gene W Yeo

doi:10.1016/j.neuron.2024.10.007

Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes

Neuron. 2024 Dec 18;112(24):4033-4047.e8. doi: 10.1016/j.neuron.2024.10.007. Epub 2024 Oct 31.

Authors

Norah Al-Azzam¹, Jenny H To², Vaishali Gautam², Lena A Street³, Chloe B Nguyen², Jack T Naritomi², Dylan C Lam⁴, Assael A Madrigal⁵, Benjamin Lee², Wenhao Jin⁶, Anthony Avina², Orel Mizrahi², Jasmine R Mueller², Willard Ford², Cara R Schiavon⁷, Elena Rebollo⁷, Anthony Q Vu², Steven M Blue², Yashwin L Madakamutil², Uri Manor⁷, Jeffrey D Rothstein⁸, Alyssa N Coyne⁸, Marko Jovanovic³, Gene W Yeo⁹

Affiliations

¹ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, San Diego, CA, USA.
² Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
³ Department of Biological Sciences, Columbia University, New York, NY, USA.
⁴ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Sanford Laboratories for Innovative Medicines, San Diego, CA, USA.
⁵ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Department of Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
⁶ Sanford Laboratories for Innovative Medicines, San Diego, CA, USA.
⁷ Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA; Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
⁸ Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁹ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Sanford Laboratories for Innovative Medicines, San Diego, CA, USA. Electronic address: [email protected].

PMID: 39486415
DOI: 10.1016/j.neuron.2024.10.007

Abstract

Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization of charged multivesicular body protein 7 (CHMP7), a protein involved in nuclear pore surveillance, has been identified as a key factor damaging nuclear pores and disrupting transport. Using CRISPR-based microRaft, followed by gRNA identification (CRaft-ID), we discovered 55 RNA-binding proteins (RBPs) that influence CHMP7 localization, including SmD1, a survival of motor neuron (SMN) complex component. Immunoprecipitation-mass spectrometry (IP-MS) and enhanced crosslinking and immunoprecipitation (CLIP) analyses revealed CHMP7's interactions with SmD1, small nuclear RNAs, and splicing factor mRNAs in motor neurons (MNs). ALS induced pluripotent stem cell (iPSC)-MNs show reduced SmD1 expression, and inhibiting SmD1/SMN complex increased CHMP7 nuclear localization. Crucially, overexpressing SmD1 in ALS iPSC-MNs restored CHMP7's cytoplasmic localization and corrected STMN2 splicing. Our findings suggest that early ALS pathogenesis is driven by SMN complex dysregulation.

Keywords: ALS; CHMP7; CRISPR screen; RNA splicing; SMN complex; SmD1; TDP-43; amyotrophic lateral sclerosis; neurodegeneration.

MeSH terms

Active Transport, Cell Nucleus
Amyotrophic Lateral Sclerosis* / genetics
Amyotrophic Lateral Sclerosis* / metabolism
Amyotrophic Lateral Sclerosis* / pathology
Cell Nucleus / metabolism
DNA-Binding Proteins* / genetics
DNA-Binding Proteins* / metabolism
Humans
Induced Pluripotent Stem Cells* / metabolism
Motor Neurons* / metabolism
Phenotype
RNA Splicing*
RNA-Binding Proteins* / genetics
RNA-Binding Proteins* / metabolism

Substances

DNA-Binding Proteins
RNA-Binding Proteins
TARDBP protein, human