Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis

  1. Gerdien Mijnheer
  2. Nila Hendrika Servaas
  3. Jing Yao Leong
  4. Arjan Boltjes
  5. Eric Spierings
  6. Phyllis Chen
  7. Liyun Lai
  8. Alessandra Petrelli
  9. Sebastiaan Vastert
  10. Rob J de Boer
  11. Salvatore Albani
  12. Aridaman Pandit  Is a corresponding author
  13. Femke van Wijk  Is a corresponding author
  1. University Medical Center Utrecht, Netherlands
  2. SingHealth Duke-NUS Academic Medical Centre, Singapore
  3. Utrecht University, Netherlands

Abstract

Autoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. Although this inflammation is often limited to specific target tissues, it remains yet to be explored whether distinct affected sites are infiltrated with the same, persistent T cell clones. Here we performed CyTOF analysis and T cell receptor (TCR) sequencing to study immune cell composition and (hyper-)expansion of circulating and joint-derived Tregs and non-Tregs in Juvenile Idiopathic Arthritis (JIA). We studied different joints affected at the same time, as well as over the course of relapsing-remitting disease. We found that the composition and functional characteristics of immune infiltrates are strikingly similar between joints within one patient, and observed a strong overlap between dominant T cell clones, especially Treg, of which some could also be detected in circulation and persisted over the course of relapsing remitting disease. Moreover, these T cell clones were characterized by a high degree of sequence similarity, indicating the presence of TCR clusters responding to the same antigens. These data suggest that in localized autoimmune disease there is auto-antigen driven expansion of both Teffector and Treg clones, that are highly persistent and are (re)circulating. These dominant clones might represent interesting therapeutic targets.

Data availability

TCR-sequencing data presented in this study have been deposited in NCBI's Gene Expression Omnibus (GEO) database under GSE196301. Both raw data and processed data are available.

The following data sets were generated

Article and author information

Author details

  1. Gerdien Mijnheer

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  2. Nila Hendrika Servaas

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9825-7554
  3. Jing Yao Leong

    Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  4. Arjan Boltjes

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  5. Eric Spierings

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9441-1019
  6. Phyllis Chen

    Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  7. Liyun Lai

    Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  8. Alessandra Petrelli

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  9. Sebastiaan Vastert

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  10. Rob J de Boer

    Theoretical Biology, Utrecht University, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2130-691X
  11. Salvatore Albani

    Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  12. Aridaman Pandit

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    For correspondence
    A.Pandit@umcutrecht.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2057-9737
  13. Femke van Wijk

    Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
    For correspondence
    F.vanWijk@umcutrecht.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8343-1356

Funding

ZonMw (91714332)

  • Femke van Wijk

Netherlands Organisation for Scientific Research (016.Veni.178.027)

  • Aridaman Pandit

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

Ethics

Human subjects: Informed consent was obtained from all patients either directly or from parents/guardians when the patients were younger than 12 years of age. The study was conducted in accordance with the Institutional Review Board of the University Medical Center Utrecht (approval no. 11-499/C), in compliance with the Declaration of Helsinki.

Copyright

© 2023, Mijnheer 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

  • 1,054
    views
  • 203
    downloads
  • 6
    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. Gerdien Mijnheer
  2. Nila Hendrika Servaas
  3. Jing Yao Leong
  4. Arjan Boltjes
  5. Eric Spierings
  6. Phyllis Chen
  7. Liyun Lai
  8. Alessandra Petrelli
  9. Sebastiaan Vastert
  10. Rob J de Boer
  11. Salvatore Albani
  12. Aridaman Pandit
  13. Femke van Wijk
(2023)
Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis
eLife 12:e79016.
https://doi.org/10.7554/eLife.79016

Share this article

https://doi.org/10.7554/eLife.79016

Further reading

    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.

    1. Immunology and Inflammation
    Hong Yu, Hiroshi Nishio ... Drew Pardoll
    Research Article

    The adaptive T cell response is accompanied by continuous rewiring of the T cell’s electric and metabolic state. Ion channels and nutrient transporters integrate bioelectric and biochemical signals from the environment, setting cellular electric and metabolic states. Divergent electric and metabolic states contribute to T cell immunity or tolerance. Here, we report in mice that neuritin (Nrn1) contributes to tolerance development by modulating regulatory and effector T cell function. Nrn1 expression in regulatory T cells promotes its expansion and suppression function, while expression in the T effector cell dampens its inflammatory response. Nrn1 deficiency in mice causes dysregulation of ion channel and nutrient transporter expression in Treg and effector T cells, resulting in divergent metabolic outcomes and impacting autoimmune disease progression and recovery. These findings identify a novel immune function of the neurotrophic factor Nrn1 in regulating the T cell metabolic state in a cell context-dependent manner and modulating the outcome of an immune response.