Quantifying changes in the T cell receptor repertoire during thymic development

  1. Francesco Camaglia
  2. Arie Ryvkin
  3. Erez Greenstein
  4. Shlomit Reich-Zeliger
  5. Benny Chain
  6. Thierry Mora  Is a corresponding author
  7. Aleksandra M Walczak  Is a corresponding author
  8. Nir Friedman
  1. CNRS, France
  2. Weizmann Institute of Science, Israel
  3. University College London, United Kingdom

Abstract

One of the feats of adaptive immunity is its ability to recognize foreign pathogens while sparing the self. During maturation in the thymus, T cells are selected through the binding properties of their antigen-specific T-cell receptor (TCR), through the elimination of both weakly (positive selection) and strongly (negative selection) self-reactive receptors. However, the impact of thymic selection on the TCR repertoire is poorly understood. Here, we use transgenic Nur77-mice expressing a T-cell activation reporter to study the repertoires of thymic T cells at various stages of their development, including cells that do not pass selection. We combine high-throughput repertoire sequencing with statistical inference techniques to characterize the selection of the TCR in these distinct subsets. We find small but significant differences in the TCR repertoire parameters between the maturation stages, which recapitulate known differentiation pathways leading to the CD4+ and CD8+ subtypes. These differences can be simulated by simple models of selection acting linearly on the sequence features. We find no evidence of specific sequences or sequence motifs or features that are suppressed by negative selection. These results favour a collective or statistical model for T-cell self non-self discrimination, where negative selection biases the repertoire away from self recognition, rather than ensuring lack of self-reactivity at the single-cell level.

Data availability

All code for reproducing the figures of this paper can be found at https://github.com/statbiophys/ thymic_development_2022.git. The data has been deposited on the SRA as BioProject ID PRJNA804508 http://www.ncbi.nlm.nih.gov/bioproject/804508.

The following data sets were generated

Article and author information

Author details

  1. Francesco Camaglia

    Laboratoire de physique de l'École normale supérieure, CNRS, Paris, France
    Competing interests
    No competing interests declared.
  2. Arie Ryvkin

    Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  3. Erez Greenstein

    Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6923-8469
  4. Shlomit Reich-Zeliger

    Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  5. Benny Chain

    Division of Infection and Immunity, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7417-3970
  6. Thierry Mora

    Laboratoire de physique de l'École normale supérieure, CNRS, Paris, France
    For correspondence
    thierry.mora@phys.ens.fr
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5456-9361
  7. Aleksandra M Walczak

    Laboratoire de physique de l'École normale supérieure, CNRS, Paris, France
    For correspondence
    aleksandra.walczak@phys.ens.fr
    Competing interests
    Aleksandra M Walczak, Senior editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2686-5702
  8. Nir Friedman

    Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.

Funding

CNRS-Weizmann (80 prime)

  • Francesco Camaglia

European Research Council (COG 724208)

  • Aleksandra M Walczak

Agence Nationale de la Recherche (ANR-19-CE45-0018)

  • Thierry Mora

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

Reviewing Editor

  1. Frederik Graw, Heidelberg University, Germany

Ethics

Animal experimentation: The experiment was carried out using three 6-weeks old male inbred Nur77-GFP/Foxp3-mCherry (C57BL/6 background). The cross was bred and maintained at the Weizmann institute. All animals were handled according to Weizmann Institute's Animal Care guide- lines, in compliance with national and international regulations. This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols ({\#}21661115-2) of the Weizmann Institute of Science. The protocol was approved by the Committee on the Ethics of Animal Experiments of the Weizmann Institute of Science. Every effort was made to minimize suffering.

Version history

  1. Preprint posted: February 15, 2022 (view preprint)
  2. Received: July 5, 2022
  3. Accepted: January 18, 2023
  4. Accepted Manuscript published: January 20, 2023 (version 1)
  5. Version of Record published: February 16, 2023 (version 2)

Copyright

© 2023, Camaglia 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

  • 2,069
    views
  • 281
    downloads
  • 9
    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. Francesco Camaglia
  2. Arie Ryvkin
  3. Erez Greenstein
  4. Shlomit Reich-Zeliger
  5. Benny Chain
  6. Thierry Mora
  7. Aleksandra M Walczak
  8. Nir Friedman
(2023)
Quantifying changes in the T cell receptor repertoire during thymic development
eLife 12:e81622.
https://doi.org/10.7554/eLife.81622

Share this article

https://doi.org/10.7554/eLife.81622

Further reading

    1. Immunology and Inflammation
    Zhixin Jing, Phillip Galbo ... David Fooksman
    Research Article

    Durable serological memory following vaccination is critically dependent on the production and survival of long-lived plasma cells (LLPCs). Yet, the factors that control LLPC specification and survival remain poorly resolved. Using intravital two-photon imaging, we find that in contrast to most plasma cells (PCs) in the bone marrow (BM), LLPCs are uniquely sessile and organized into clusters that are dependent on APRIL, an important survival factor. Using deep, bulk RNA sequencing, and surface protein flow-based phenotyping, we find that LLPCs express a unique transcriptome and phenotype compared to bulk PCs, fine-tuning expression of key cell surface molecules, CD93, CD81, CXCR4, CD326, CD44, and CD48, important for adhesion and homing. Conditional deletion of Cxcr4 in PCs following immunization leads to rapid mobilization from the BM, reduced survival of antigen-specific PCs, and ultimately accelerated decay of antibody titer. In naïve mice, the endogenous LLPCs BCR repertoire exhibits reduced diversity, reduced somatic mutations, and increased public clones and IgM isotypes, particularly in young mice, suggesting LLPC specification is non-random. As mice age, the BM PC compartment becomes enriched in LLPCs, which may outcompete and limit entry of new PCs into the LLPC niche and pool.

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Ffion R Hammond, Amy Lewis ... Philip M Elks
    Research Article

    Tuberculosis is a major global health problem and is one of the top 10 causes of death worldwide. There is a pressing need for new treatments that circumvent emerging antibiotic resistance. Mycobacterium tuberculosis parasitises macrophages, reprogramming them to establish a niche in which to proliferate, therefore macrophage manipulation is a potential host-directed therapy if druggable molecular targets could be identified. The pseudokinase Tribbles1 (Trib1) regulates multiple innate immune processes and inflammatory profiles making it a potential drug target in infections. Trib1 controls macrophage function, cytokine production, and macrophage polarisation. Despite wide-ranging effects on leukocyte biology, data exploring the roles of Tribbles in infection in vivo are limited. Here, we identify that human Tribbles1 is expressed in monocytes and is upregulated at the transcript level after stimulation with mycobacterial antigen. To investigate the mechanistic roles of Tribbles in the host response to mycobacteria in vivo, we used a zebrafish Mycobacterium marinum (Mm) infection tuberculosis model. Zebrafish Tribbles family members were characterised and shown to have substantial mRNA and protein sequence homology to their human orthologues. trib1 overexpression was host-protective against Mm infection, reducing burden by approximately 50%. Conversely, trib1 knockdown/knockout exhibited increased infection. Mechanistically, trib1 overexpression significantly increased the levels of proinflammatory factors il-1β and nitric oxide. The host-protective effect of trib1 was found to be dependent on the E3 ubiquitin kinase Cop1. These findings highlight the importance of Trib1 and Cop1 as immune regulators during infection in vivo and suggest that enhancing macrophage TRIB1 levels may provide a tractable therapeutic intervention to improve bacterial infection outcomes in tuberculosis.