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

Abstract
Data availability
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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-Akt^S473-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

1. Yang C
2. Siebert JR
3. Burns R
4. Zheng Y
5. Mei A
6. Bonacci B
7. Wang D
8. Urrutia RA
9. Riese MJ
10. Rao S
11. Carlson K
12. Thakar MS
13. Malarkannan S
(2020) Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature the immature NK gene signature
NCBI Gene Expression Omnibus, GSE150166.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150166

The following previously published data sets were used

1. Yang C
2. Tsaih SW
3. Lemke A
4. Flister MJ
5. Thakar MS
6. Malarkannan S
(2018) mTORC1 and mTORC2 differentially regulate NK cell development
NCBI SRA BioSample database, PRJNA434424.

https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA434424
1. Shih HY
2. Sciume G
3. Mikami Y
4. Guo L
5. Sun HW
6. Brooks SR
7. Urban JF
8. Davis FP
9. Kanno Y
10. O'Shea JJ
(2016) Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality
NCBI Gene Expression Omnibus, GSE77695.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77695

Article and author information

Author details

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.
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.
Robert Burns

Blood Research Institute, Versiti Blood Research Institute, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
Yongwei Zheng

Laboratory of B-Cell Lymphopoiesis, Versiti Blood Research Institute, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
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.
Benedetta Bonacci

Flow Cytometry Core, Versiti Blood Research Institute, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
Demin Wang

Laboratory of B-Cell Lymphopoiesis, Versiti Blood Research Institute, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
Raul A Urrutia

Surgery, Medical College of Wisconsin, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
Matthew J Riese

Laboratory of Lymphocyte Biology, Versiti Blood Research Institute, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
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.
Karen-Sue Carlson

Laboratory of Coagulation Biology, Versiti Blood Research Institute, Milwaukee, United States

Competing interests
The authors declare that no competing interests exist.
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.
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.

"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.

Copyright

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.