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Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node

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Cite this article as: eLife 2021;10:e62781 doi: 10.7554/eLife.62781

Abstract

The detection of foreign antigens in vivo has relied on fluorescent conjugation or indirect read-outs such as antigen presentation. In our studies, we found that these widely used techniques had several technical limitations that have precluded a complete picture of antigen trafficking or retention across lymph node cell types. To address these limitations, we developed a 'molecular tracking device' to follow the distribution, acquisition, and retention of antigen in the lymph node. Utilizing an antigen conjugated to a nuclease-resistant DNA tag, acting as a combined antigen-adjuvant conjugate, and single-cell mRNA sequencing we quantified antigen abundance in lymph node. Variable antigen levels enabled the identification of caveolar endocytosis as a mechanism of antigen acquisition or retention in lymphatic endothelial cells. Thus, these molecular tracking devices enable new approaches to study dynamic tissue dissemination of antigen-adjuvant conjugates and identify new mechanisms of antigen acquisition and retention at cellular resolution in vivo.

Data availability

Raw and processed data for this study have been deposited at NCBI GEO under accession GSE150719. A reproducible analysis pipeline is available at https://github.com/rnabioco/antigen-tracking.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Shannon M Walsh

    Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9845-629X
  2. Ryan M Sheridan

    RNA Biosciences Initiative, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Erin D Lucas

    Medicine/Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Thu A Doan

    Medicine/Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Brian C Ware

    Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Johnathon Schafer

    Medicine/Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Rui Fu

    RNA bioscience initiative, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Matthew A Burchill

    Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Jay R Hesselberth

    Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6299-179X
  10. Beth Ann Jiron Tamburini

    Medicine/Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, United States
    For correspondence
    beth.tamburini@cuanschutz.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1991-231X

Funding

National Institutes of Health (R01 AI121209)

  • Beth Ann Jiron Tamburini

University of Colorado Department of Medicine Outstanding Early Career Scholar and RBI Clinical Scholar Award (Outstanding Early Career Scholar and RBI Clinical Scholar Award)

  • Beth Ann Jiron Tamburini

American Cancer Society (Post-doctoral Fellowship)

  • Shannon M Walsh

National Institutes of Health (T32 AI007405)

  • Erin D Lucas

National Institutes of Health (R35 GM119550)

  • Jay R Hesselberth

National Institutes of Health (T32 AI074491)

  • Ryan M Sheridan

National Institutes of Health (R21 AI155929)

  • Jay R Hesselberth
  • Beth Ann Jiron Tamburini

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 animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Colorado under protocol number 00067.

Reviewing Editor

  1. Michael L Dustin, University of Oxford, United Kingdom

Publication history

  1. Received: September 4, 2020
  2. Accepted: April 9, 2021
  3. Accepted Manuscript published: April 12, 2021 (version 1)
  4. Version of Record published: May 12, 2021 (version 2)

Copyright

© 2021, Walsh 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.

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