Inducible and reversible inhibition of miRNA-mediated gene repression in vivo

  1. Gaspare La Rocca  Is a corresponding author
  2. Bryan King
  3. Bing Shui
  4. Xiaoyi Li
  5. Minsi Zhang
  6. Kemal Akat
  7. Paul Ogrodowski
  8. Chiara Mastroleo
  9. Kevin Chen
  10. Vincenzo Cavalieri
  11. Yilun Ma
  12. Viviana Anelli
  13. Doron Betel
  14. Joana Vidigal
  15. Thomas Tuschl
  16. Gunter Meister
  17. Craig B Thompson
  18. Tullia Lindsten
  19. Kevin Haigis
  20. Andrea Ventura  Is a corresponding author
  1. Memorial Sloan Kettering Cancer Center, United States
  2. Dana Farber Cancer Institute, United States
  3. Rockefeller University, United States
  4. University of Palermo, Italy
  5. Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, United States
  6. Center of Integrative Biology, University of Trento, Italy
  7. Weill Cornell Medical College, United States
  8. NCI, NIH, United States
  9. Max Planck Institute of Biochemistry, Germany
  10. Memorial Sloan-Kettering Cancer Center, United States

Abstract

Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss of function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.

Data availability

Processed sequencing data are included as source data. Fastq files have been deposited to GEO (GEO accession number: GSE179588)

The following previously published data sets were used

Article and author information

Author details

  1. Gaspare La Rocca

    Memorial Sloan Kettering Cancer Center, New York, United States
    For correspondence
    laroccag@mskcc.org
    Competing interests
    No competing interests declared.
  2. Bryan King

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  3. Bing Shui

    Cancer Biology, Dana Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5956-130X
  4. Xiaoyi Li

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  5. Minsi Zhang

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  6. Kemal Akat

    Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9012-3551
  7. Paul Ogrodowski

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  8. Chiara Mastroleo

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  9. Kevin Chen

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0674-1411
  10. Vincenzo Cavalieri

    Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
    Competing interests
    No competing interests declared.
  11. Yilun Ma

    Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, United States
    Competing interests
    No competing interests declared.
  12. Viviana Anelli

    Center of Integrative Biology, University of Trento, Trento, Italy
    Competing interests
    No competing interests declared.
  13. Doron Betel

    Medicine and Institution for Computational Biomedicine, Weill Cornell Medical College, New York, United States
    Competing interests
    No competing interests declared.
  14. Joana Vidigal

    NCI, NIH, Bethesda, United States
    Competing interests
    No competing interests declared.
  15. Thomas Tuschl

    Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  16. Gunter Meister

    Max Planck Institute of Biochemistry, Regensburg, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2098-9923
  17. Craig B Thompson

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    Craig B Thompson, is a founder of Agios Pharmaceuticals and a member of its scientific advisory board. He is also a former member of the Board of Directors and stockholder of Merck and Charles River Laboratories. He is a named inventor on patents related to cellular metabolism. Potentially relevant patents on which he is a named inventor include the following: (i) L-2-hydroxyglutarate and stress induced metabolism (United States Patent #10,450,596). (ii) Single diastereomers of 4-fluoroglutamine and methods of their preparation and use (United States Patent #8,747,809). A complete list of patents can be found at the following link: https://tinyurl.com/y35qvajq..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3580-2751
  18. Tullia Lindsten

    Immunology, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  19. Kevin Haigis

    Cancer Biology, Dana Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  20. Andrea Ventura

    Memorial Sloan Kettering Cancer Center, New York, United States
    For correspondence
    venturaa@mskcc.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4320-9907

Funding

National Cancer Institute (R01CA149707)

  • Andrea Ventura

National Cancer Institute (R01CA245507)

  • Andrea Ventura

National Cancer Institute (P30 CA008748)

  • Craig B Thompson

Starr Foundation (NA)

  • Gaspare La Rocca
  • Tullia Lindsten
  • Andrea Ventura

National Institute of General Medical Sciences (T32GM007739)

  • Yilun Ma

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

Ethics

Animal experimentation: This study was performed in strict 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 (#10-10-022) of Memorial Sloan Kettering Cancer Center

Reviewing Editor

  1. Ashish Lal, National Institutes of Health, United States

Publication history

  1. Preprint posted: June 1, 2021 (view preprint)
  2. Received: June 3, 2021
  3. Accepted: August 24, 2021
  4. Accepted Manuscript published: August 31, 2021 (version 1)
  5. Version of Record published: September 27, 2021 (version 2)

Copyright

© 2021, La Rocca 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. Gaspare La Rocca
  2. Bryan King
  3. Bing Shui
  4. Xiaoyi Li
  5. Minsi Zhang
  6. Kemal Akat
  7. Paul Ogrodowski
  8. Chiara Mastroleo
  9. Kevin Chen
  10. Vincenzo Cavalieri
  11. Yilun Ma
  12. Viviana Anelli
  13. Doron Betel
  14. Joana Vidigal
  15. Thomas Tuschl
  16. Gunter Meister
  17. Craig B Thompson
  18. Tullia Lindsten
  19. Kevin Haigis
  20. Andrea Ventura
(2021)
Inducible and reversible inhibition of miRNA-mediated gene repression in vivo
eLife 10:e70948.
https://doi.org/10.7554/eLife.70948

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