Ubiquitination and degradation of NF90 by Tim-3 inhibits antiviral innate immunity

  1. Shuaijie Dou
  2. Guoxian Li
  3. Ge Li
  4. Chunmei Hou
  5. Yang Zheng
  6. Lili Tang
  7. Yang Gao
  8. Rongliang Mo
  9. Yuxiang Li
  10. Renxi Wang  Is a corresponding author
  11. Beifen Shen
  12. Jun Zhang  Is a corresponding author
  13. Gencheng Han  Is a corresponding author
  1. Beijing Institute of Basic and Medical Sciences, China
  2. First hospital of Jilin University, China
  3. Beijing Institute of Basic Medical Sciences, China
  4. Medical School of Henan University,, China

Abstract

Nuclear Factor 90 (NF90) is a novel virus sensor that serves to initiate antiviral innate immunity by triggering the stress granules (SGs) formation. However, the regulation of the NF90-SGs pathway remain largely unclear. We found that Tim-3, an immune checkpoint inhibitor, promotes the ubiquitination and degradation of NF90 and inhibits NF90-SGs mediated antiviral immunity. Vesicular Stomatitis Virus (VSV) infection induces the up-regulation and activation of Tim-3 in macrophages which in turn recruited the E3 ubiquitin ligase TRIM47 to the zinc finger domain of NF90 and initiated a proteasome-dependent degradation via K48-linked ubiquitination at Lys297. Targeted inactivation of the Tim-3 enhances the NF90 downstream SGs formation by selectively increasing the phosphorylation of PKR and eIF2a, the expression of SGs markers G3BP1 and TIA-1, and protected mice from VSV challenge. These findings provide insights into the crosstalk between Tim-3 and other receptors in antiviral innate immunity and its related clinical significance.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Shuaijie Dou

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Guoxian Li

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Ge Li

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Chunmei Hou

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Yang Zheng

    4.Department of Oncology,, First hospital of Jilin University, Department of Oncology,, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Lili Tang

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Yang Gao

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Rongliang Mo

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Yuxiang Li

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Renxi Wang

    Laboratory of Immunology, Beijing Institute of Basic Medical Sciences, Beijing, China
    For correspondence
    wang_renxi@hotmail.com
    Competing interests
    The authors declare that no competing interests exist.
  11. Beifen Shen

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  12. Jun Zhang

    Institute of Immunology,, Medical School of Henan University,, Kaifeng, China
    For correspondence
    zhangjun@henu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
  13. Gencheng Han

    Immunology, Beijing Institute of Basic and Medical Sciences, Beijing, China
    For correspondence
    genchenghan@163.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1408-878X

Funding

This work was supported by the National Natural Sciences Foundation of China (grants no. 81971473, 81771684), and the Beijing Natural Sciences Foundation (grant no.7192145).

Ethics

Animal experimentation: The protocol was approved by the Ethics Committee of Animal Experiments of the Beijing Institute of Brain Sciences( (IACUC-DWZX-2018-645). All efforts were made to minimize suffering.

Copyright

© 2021, Dou 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.

Metrics

  • 893
    views
  • 189
    downloads
  • 15
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Shuaijie Dou
  2. Guoxian Li
  3. Ge Li
  4. Chunmei Hou
  5. Yang Zheng
  6. Lili Tang
  7. Yang Gao
  8. Rongliang Mo
  9. Yuxiang Li
  10. Renxi Wang
  11. Beifen Shen
  12. Jun Zhang
  13. Gencheng Han
(2021)
Ubiquitination and degradation of NF90 by Tim-3 inhibits antiviral innate immunity
eLife 10:e66501.
https://doi.org/10.7554/eLife.66501

Share this article

https://doi.org/10.7554/eLife.66501

Further reading

    1. Computational and Systems Biology
    2. Immunology and Inflammation
    Peng Li, Sree Pulugulla ... Warren J Leonard
    Short Report

    Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human IL10 gene, which harbors a non-canonical IKZF1 binding site. We confirmed the cooperative binding of JUN and IKZF1 and showed that the activity of an IL10-luciferase reporter construct in primary B and T cells depended on both this site and the AP1 binding site within this composite element. Overall, our findings reveal an unappreciated global association of IKZF1 and AP1 and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.

    1. Immunology and Inflammation
    2. Medicine
    Edwin A Homan, Ankit Gilani ... James C Lo
    Short Report

    Together with obesity and type 2 diabetes, metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing global epidemic. Activation of the complement system and infiltration of macrophages has been linked to progression of metabolic liver disease. The role of complement receptors in macrophage activation and recruitment in MASLD remains poorly understood. In human and mouse, C3AR1 in the liver is expressed primarily in Kupffer cells, but is downregulated in humans with MASLD compared to obese controls. To test the role of complement 3a receptor (C3aR1) on macrophages and liver resident macrophages in MASLD, we generated mice deficient in C3aR1 on all macrophages (C3aR1-MφKO) or specifically in liver Kupffer cells (C3aR1-KpKO) and subjected them to a model of metabolic steatotic liver disease. We show that macrophages account for the vast majority of C3ar1 expression in the liver. Overall, C3aR1-MφKO and C3aR1-KpKO mice have similar body weight gain without significant alterations in glucose homeostasis, hepatic steatosis and fibrosis, compared to controls on a MASLD-inducing diet. This study demonstrates that C3aR1 deletion in macrophages or Kupffer cells, the predominant liver cell type expressing C3ar1, has no significant effect on liver steatosis, inflammation or fibrosis in a dietary MASLD model.