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

  • 886
    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. Immunology and Inflammation
    Josep Garnica, Patricia Sole ... Pere Santamaria
    Research Article

    Chronic antigenic stimulation can trigger the formation of interleukin 10 (IL-10)-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that murine T-follicular helper (TFH) cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is characterized by the progressive loss and acquisition of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Here, we use a broad range of bulk and single-cell transcriptional and epigenetic tools to investigate the epigenetic underpinnings of this process. At the single-cell level, the TFH-to-TR1 cell transition is accompanied by both, downregulation of TFH cell-specific gene expression due to loss of chromatin accessibility, and upregulation of TR1 cell-specific genes linked to chromatin regions that remain accessible throughout the transdifferentiation process, with minimal generation of new open chromatin regions. By interrogating the epigenetic status of accessible TR1 genes on purified TFH and conventional T-cells, we find that most of these genes, including Il10, are already poised for expression at the TFH cell stage. Whereas these genes are closed and hypermethylated in Tconv cells, they are accessible, hypomethylated, and enriched for H3K27ac-marked and hypomethylated active enhancers in TFH cells. These enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors TOX-2, IRF4, and c-MAF. Together, these data suggest that the TR1 gene expression program is genetically imprinted at the TFH cell stage.

    1. Genetics and Genomics
    2. Immunology and Inflammation
    Stephanie Guillet, Tomi Lazarov ... Frédéric Geissmann
    Research Article

    Systemic lupus erythematosus (SLE) is an autoimmune disease, the pathophysiology and genetic basis of which are incompletely understood. Using a forward genetic screen in multiplex families with SLE, we identified an association between SLE and compound heterozygous deleterious variants in the non-receptor tyrosine kinases (NRTKs) ACK1 and BRK. Experimental blockade of ACK1 or BRK increased circulating autoantibodies in vivo in mice and exacerbated glomerular IgG deposits in an SLE mouse model. Mechanistically, NRTKs regulate activation, migration, and proliferation of immune cells. We found that the patients’ ACK1 and BRK variants impair efferocytosis, the MERTK-mediated anti-inflammatory response to apoptotic cells, in human induced pluripotent stem cell (hiPSC)-derived macrophages, which may contribute to SLE pathogenesis. Overall, our data suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis in macrophages.