HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness

  1. Jessica SY Ho
  2. Federico Di Tullio
  3. Megan Schwarz
  4. Diana Low
  5. Danny Incarnato
  6. Florence Gay
  7. Tommaso Tabaglio
  8. JingXian Zhang
  9. Heike Wollmann
  10. Leilei Chen
  11. Omer An
  12. Tim Hon Man Chan
  13. Alexander Hall Hickman
  14. Simin Zheng
  15. Vladimir Roudko
  16. Sujun Chen
  17. Alcida Karz
  18. Musaddeque Ahmed
  19. Housheng Hansen He
  20. Benjamin D Greenbaum
  21. Salvatore Oliviero
  22. Michela Serresi
  23. Gaetano Gargiulo
  24. Karen M Mann
  25. Eva Hernando
  26. David Mulholland
  27. Ivan Marazzi
  28. Dave Keng Boon Wee
  29. Ernesto Guccione  Is a corresponding author
  1. Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
  2. Icahn School of Medicine, United States
  3. Icahn School of Medicine at Mount Sinai, United States
  4. IIGM (Italian Institute for Genomic Medicine), Italy
  5. Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
  6. Cancer Science Institute of Singapore, National University of Singapore, Singapore
  7. Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
  8. School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
  9. University of Toronto, Canada
  10. NYU, United States
  11. Italian Institute for Genomic Medicine, Italy
  12. Max Delbruck Center for Molecular Medicine, Germany
  13. H Lee Moffitt Cancer Center and Research Institute;, United States
  14. Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore., Singapore

Abstract

High spliceosome activity is a dependency for cancer cells, making them more vulnerable to perturbation of the splicing machinery compared to normal cells. To identify splicing factors important for prostate cancer (PCa) fitness, we performed pooled shRNA screens in vitro and in vivo. Our screens identified HNRNPM as a regulator of PCa cell growth. RNA- and eCLIP-sequencing identified HNRNPM binding to transcripts of key homeostatic genes. HNRNPM binding to its targets prevents aberrant exon inclusion and back-splicing events. In both linear and circular mis-spliced transcripts, HNRNPM preferentially binds to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent linear splicing events using splice-switching-antisense-oligonucleotides (SSOs) was sufficient to inhibit PCa cell growth. This suggests that PCa dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Our results have further been confirmed in other solid tumors. Taken together, our data reveal a role for HNRNPM in supporting cancer cell fitness. Inhibition of HNRNPM activity is therefore a potential therapeutic strategy in suppressing growth of PCa and other solid tumors.

Data availability

All data needed to evaluate the conclusions in this study are present in the paper and/or its Supplementary Materials. eCLIP and RNA-Sequencing data supporting the findings of this study have been deposited into the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus under accessions GSE113786.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Jessica SY Ho

    Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  2. Federico Di Tullio

    Icahn School of Medicine, NY, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Megan Schwarz

    Icahn School of Medicine at Mount Sinai, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Diana Low

    Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  5. Danny Incarnato

    IIGM (Italian Institute for Genomic Medicine), Torino, Italy
    Competing interests
    The authors declare that no competing interests exist.
  6. Florence Gay

    Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  7. Tommaso Tabaglio

    Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  8. JingXian Zhang

    Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  9. Heike Wollmann

    Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  10. Leilei Chen

    Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  11. Omer An

    Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  12. Tim Hon Man Chan

    Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  13. Alexander Hall Hickman

    Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  14. Simin Zheng

    School of Biological Sciences, Nanyang Technological University, Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  15. Vladimir Roudko

    Icahn School of Medicine at Mount Sinai, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Sujun Chen

    University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  17. Alcida Karz

    NYU, NY, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Musaddeque Ahmed

    University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  19. Housheng Hansen He

    University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  20. Benjamin D Greenbaum

    Icahn School of Medicine at Mount Sinai, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  21. Salvatore Oliviero

    Italian Institute for Genomic Medicine, Torino, Italy
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3405-765X
  22. Michela Serresi

    Max Delbruck Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  23. Gaetano Gargiulo

    Max Delbruck Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  24. Karen M Mann

    H Lee Moffitt Cancer Center and Research Institute;, Tampa, United States
    Competing interests
    The authors declare that no competing interests exist.
  25. Eva Hernando

    NYU, NY, United States
    Competing interests
    The authors declare that no competing interests exist.
  26. David Mulholland

    Icahn School of Medicine at Mount Sinai, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  27. Ivan Marazzi

    Icahn School of Medicine at Mount Sinai, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  28. Dave Keng Boon Wee

    Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore., Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  29. Ernesto Guccione

    Icahn School of Medicine at Mount Sinai, New York, United States
    For correspondence
    ernesto.guccione@mssm.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7764-5307

Funding

National Cancer Institute (R01CA197910)

  • David Mulholland

National Medical Research Council (NMRC/OFIRG/0032/2017)

  • Dave Keng Boon Wee
  • Ernesto Guccione

National Research Foundation Singapore (NRF-CRP17-2017-06)

  • Dave Keng Boon Wee
  • Ernesto Guccione

National Cancer Institute (R01CA249204)

  • Ernesto Guccione

ISMMS

  • Ernesto Guccione

Melanoma Research Alliance (MRA Team Science Award)

  • Eva Hernando
  • Ernesto Guccione

Lee Kuan Postdoctural Fellowship

  • Simin Zheng

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

Reviewing Editor

  1. Juan Valcárcel, Centre de Regulació Genòmica (CRG), Spain

Version history

  1. Received: June 4, 2020
  2. Accepted: May 30, 2021
  3. Accepted Manuscript published: June 2, 2021 (version 1)
  4. Version of Record published: August 6, 2021 (version 2)

Copyright

© 2021, Ho 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. Jessica SY Ho
  2. Federico Di Tullio
  3. Megan Schwarz
  4. Diana Low
  5. Danny Incarnato
  6. Florence Gay
  7. Tommaso Tabaglio
  8. JingXian Zhang
  9. Heike Wollmann
  10. Leilei Chen
  11. Omer An
  12. Tim Hon Man Chan
  13. Alexander Hall Hickman
  14. Simin Zheng
  15. Vladimir Roudko
  16. Sujun Chen
  17. Alcida Karz
  18. Musaddeque Ahmed
  19. Housheng Hansen He
  20. Benjamin D Greenbaum
  21. Salvatore Oliviero
  22. Michela Serresi
  23. Gaetano Gargiulo
  24. Karen M Mann
  25. Eva Hernando
  26. David Mulholland
  27. Ivan Marazzi
  28. Dave Keng Boon Wee
  29. Ernesto Guccione
(2021)
HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness
eLife 10:e59654.
https://doi.org/10.7554/eLife.59654

Share this article

https://doi.org/10.7554/eLife.59654

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