Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature

  1. Chao Yang
  2. Jason R Siebert
  3. Robert Burns
  4. Yongwei Zheng
  5. Ao Mei
  6. Benedetta Bonacci
  7. Demin Wang
  8. Raul A Urrutia
  9. Matthew J Riese
  10. Sridhar Rao
  11. Karen-Sue Carlson
  12. Monica S Thakar
  13. Subramaniam Malarkannan  Is a corresponding author
  1. Versiti Blood Research Institute, United States
  2. Medical College of Wisconsin, United States

Abstract

The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based on transcriptome, we identified five distinct NK cell clusters and define their relative developmental maturity in the bone marrow. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature NK cells. Since mTORC2 regulates the expression of T-bet through AktS473-FoxO1 axis, we further characterized the T-bet-deficient NK cells and found an augmented immature transcriptomic signature. Moreover, deletion of Foxo1 restores the expression of T-bet and corrects the abnormal expression of immature NK genes. Collectively, our study reveals a novel role for mTORC2-AktS473-FoxO1-T-bet axis in suppressing the transcriptional signature of immature NK cells.

Data availability

Sequencing data have been deposited in GEO under accession code GSE150166

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

Article and author information

Author details

  1. Chao Yang

    Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Jason R Siebert

    Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Robert Burns

    Blood Research Institute, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Yongwei Zheng

    Laboratory of B-Cell Lymphopoiesis, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Ao Mei

    Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Benedetta Bonacci

    Flow Cytometry Core, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Demin Wang

    Laboratory of B-Cell Lymphopoiesis, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Raul A Urrutia

    Surgery, Medical College of Wisconsin, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Matthew J Riese

    Laboratory of Lymphocyte Biology, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Sridhar Rao

    Laboratory of Stem Cell Transcriptional Regulation, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Karen-Sue Carlson

    Laboratory of Coagulation Biology, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Monica S Thakar

    Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Subramaniam Malarkannan

    Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, United States
    For correspondence
    subra.malar@bcw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7511-2731

Funding

National Institutes of Health (AI102893)

  • Subramaniam Malarkannan

National Cancer Institute (CA179363)

  • Subramaniam Malarkannan

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

Ethics

Animal experimentation: All mice were maintained in pathogen-free conditions in the Biological Resource Center at the Medical College of Wisconsin. All animal protocols were approved by Institutional Animal Care and Use Committees. The unique animal protocols that are approved by the IACUC and used in this study is: AUA1512.

Reviewing Editor

  1. Florent Ginhoux, Agency for Science Technology and Research, Singapore

Publication history

  1. Received: August 25, 2019
  2. Accepted: May 8, 2020
  3. Accepted Manuscript published: May 14, 2020 (version 1)
  4. Version of Record published: May 28, 2020 (version 2)

Copyright

© 2020, Yang 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. Chao Yang
  2. Jason R Siebert
  3. Robert Burns
  4. Yongwei Zheng
  5. Ao Mei
  6. Benedetta Bonacci
  7. Demin Wang
  8. Raul A Urrutia
  9. Matthew J Riese
  10. Sridhar Rao
  11. Karen-Sue Carlson
  12. Monica S Thakar
  13. Subramaniam Malarkannan
(2020)
Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature
eLife 9:e51339.
https://doi.org/10.7554/eLife.51339

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