EXOSC3 S1-domain variants implicated in PCH1b alter RNA exosome cap subunit abundance and thermal stability disrupting rRNA processing and targeting of AU-rich mRNA

  • bioRxiv. 2025 Jun 1:2025.05.31.657176. doi: 10.1101/2025.05.31.657176.
Avery M Runnebohm  1  2 ,  H R Sagara Wijeratne  1  2  3 ,  Monica P Barron  1  4 ,  Whitney R Smith-Kinnaman  1 ,  James D Rooney  1 ,  Sarah A Peck Justice  5 ,  Lauryn A Cureton  6  7 ,  Annalise Holland  6  7 ,  Homa Ghalei  6 ,  Stephane Pelletier  8 ,  Emma H Doud  1  2 ,  Jonah Z Vilseck  1  4 ,  Amber L Mosley  1  2  3  4  8
Affiliations
  • 1. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN.
  • 2. Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN.
  • 3. Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN.
  • 4. Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN.
  • 5. Department of Biology, Marian University, Indianapolis, IN.
  • 6. Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.
  • 7. Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA.
  • 8. Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN.
PMID: 40501579 DOI: 10.1101/2025.05.31.657176
Abstract

Missense variants in EXOSC3, an RNA exosome subunit, have been identified in patients with PCH1b. We investigated three missense variants in the S1 domain of EXOSC3, including one variant of uncertain significance (VUS) and two pathogenic variants (hence S1 variants). EXOSC3 S1 variant cell lines were generated using CRISPR-Cas9 resulting in widespread proteome changes including decreases in some RNA exosome subunits paired with increases in the catalytic subunit DIS3. Thermal stability, analyzed by PISA, revealed extensive destabilization of RNA exosome cap subunits and the cap-associated exonuclease EXOSC10. Functionally, S1 variants altered rRNA processing with corresponding protein compensation observed in rRNA processing proteins outside the RNA exosome. Exogenous overexpression of EXOSC3 rescues many molecular defects caused by S1 variants suggesting that protein destabilization and turnover strongly contribute to molecular defects. Overall, our findings define the mechanisms through which cells respond to EXOSC3 S1 variant disruption of RNA processing homeostasis.

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