A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS

  1. Mary McMahon
  2. Adrian Contreras
  3. Mikael Holm
  4. Tamayo Uechi
  5. Craig M Forester
  6. Xiaming Pang
  7. Cody Jackson
  8. Meredith E Calvert
  9. Bin Chen
  10. David A Quigley
  11. John M Luk
  12. R Kate Kelley
  13. John D Gordan
  14. Ryan M Gill
  15. Scott C Blanchard  Is a corresponding author
  16. Davide Ruggero  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Weill Cornell Medicine, United States
  3. Gladstone Institutes, United States
  4. Michigan State University, United States
  5. Arbele Corporation, United States

Abstract

Small nucleolar RNAs (snoRNAs) are a diverse group of non-coding RNAs that direct chemical modifications at specific residues on other RNA molecules, primarily on ribosomal RNA (rRNA). SnoRNAs are altered in several cancers; however, their role in cell homeostasis as well as in cellular transformation remains poorly explored. Here, we show that specific subsets of snoRNAs are differentially regulated during the earliest cellular response to oncogenic RASG12V expression. We describe a novel function for one H/ACA snoRNA, SNORA24, which guides two pseudouridine modifications within the small ribosomal subunit, in RAS-induced senescence in vivo. We find that in mouse models, loss of Snora24 cooperates with RASG12V to promote the development of liver cancer that closely resembles human steatohepatitic hepatocellular carcinoma. From a clinical perspective, we further show that human hepatocellular carcinomas with low SNORA24 expression display increased lipid content and are associated with poor patient survival. We next asked whether ribosomes lacking SNORA24-guided pseudouridine modifications on 18S rRNA have alterations in their biophysical properties. Single-molecule Fluorescence Resonance Energy Transfer (FRET) analyses revealed that these ribosomes exhibit perturbations in aminoacyl-transfer RNA (aa-tRNA) selection and altered pre-translocation ribosome complex dynamics. Furthermore, we find that HCC cells lacking SNORA24-guided pseudouridine modifications have increased translational miscoding and stop codon readthrough frequencies. These findings highlight a role for specific snoRNAs in safeguarding against oncogenic insult and demonstrate a functional link between H/ACA snoRNAs regulated by RAS and the biophysical properties of ribosomes in cancer.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 1 and Figure 1-figure supplement 2.

Article and author information

Author details

  1. Mary McMahon

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5548-2949
  2. Adrian Contreras

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    Adrian Contreras, Current employee of Celgene Corporation.
  3. Mikael Holm

    Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
  4. Tamayo Uechi

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  5. Craig M Forester

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  6. Xiaming Pang

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  7. Cody Jackson

    Gladstone Histology and Light Microscopy Core, Gladstone Institutes, San Francisco, United States
    Competing interests
    No competing interests declared.
  8. Meredith E Calvert

    Gladstone Histology and Light Microscopy Core, Gladstone Institutes, San Francisco, United States
    Competing interests
    No competing interests declared.
  9. Bin Chen

    Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, United States
    Competing interests
    No competing interests declared.
  10. David A Quigley

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  11. John M Luk

    Arbele Corporation, Seattle, United States
    Competing interests
    John M Luk, Current employee of Arbele Corporation.
  12. R Kate Kelley

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  13. John D Gordan

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  14. Ryan M Gill

    Department of Pathology, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  15. Scott C Blanchard

    Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
    For correspondence
    scott.blanchard@stjude.org
    Competing interests
    No competing interests declared.
  16. Davide Ruggero

    Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    For correspondence
    davide.ruggero@ucsf.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9444-5865

Funding

National Institutes of Health (R35 CA242986)

  • Davide Ruggero

National Institutes of Health (R01 GM079238-13)

  • Scott C Blanchard

National Institutes of Health (R21 TR001743)

  • Bin Chen

National Institutes of Health (K01 ES028047)

  • Bin Chen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Nahum Sonenberg, McGill University, Canada

Ethics

Animal experimentation: This study was performed in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved Institutional Animal Care and Use Committee (IACUC) protocols (AN151649) of the University of California, San Francisco, with assistance from the Laboratory Animal Resource Center (LARC).

Human subjects: This study was approved by the Institutional Review Board (IRB) of the University of California, San Francisco (UCSF). Written informed consent was obtained from every patient. Liver tissue specimens were obtained from patients undergoing treatment for HCC at UCSF.

Version history

  1. Received: May 28, 2019
  2. Accepted: September 2, 2019
  3. Accepted Manuscript published: September 3, 2019 (version 1)
  4. Version of Record published: October 3, 2019 (version 2)

Copyright

© 2019, McMahon et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Mary McMahon
  2. Adrian Contreras
  3. Mikael Holm
  4. Tamayo Uechi
  5. Craig M Forester
  6. Xiaming Pang
  7. Cody Jackson
  8. Meredith E Calvert
  9. Bin Chen
  10. David A Quigley
  11. John M Luk
  12. R Kate Kelley
  13. John D Gordan
  14. Ryan M Gill
  15. Scott C Blanchard
  16. Davide Ruggero
(2019)
A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS
eLife 8:e48847.
https://doi.org/10.7554/eLife.48847

Share this article

https://doi.org/10.7554/eLife.48847

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