Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair

  1. Justinn Barr
  2. Maria Elena Gentile
  3. Sunyoung Lee
  4. Maya E Kotas
  5. Maria Fernanda de Mello Costa
  6. Nicolas P Holcomb
  7. Abigail Jaquish
  8. Gargi Palashikar
  9. Marcella Soewignjo
  10. Margaret McDaniel
  11. Ichiro Matsumoto
  12. Robert Margolskee
  13. Jakob Von Moltke
  14. Noam A Cohen
  15. Xin Sun  Is a corresponding author
  16. Andrew E Vaughan  Is a corresponding author
  1. University of California, San Diego, United States
  2. University of Pennsylvania, United States
  3. University of California, San Francisco, United States
  4. University of Washington, United States
  5. Monell Chemical Senses Center, United States

Abstract

While the lung bears significant regenerative capacity, severe viral pneumonia can chronically impair lung function by triggering dysplastic remodeling. The connection between these enduring changes and chronic disease remains poorly understood. We recently described the emergence of tuft cells within Krt5+ dysplastic regions after influenza injury. Using bulk and single cell transcriptomics, we characterized and delineated multiple distinct tuft cell populations that arise following influenza clearance. Distinct from intestinal tuft cells which rely on Type 2 immune signals for their expansion, neither IL-25 nor IL-4ra signaling are required to drive tuft cell development in dysplastic/injured lungs. In addition, tuft cell expansion occurred independently of type I or type III interferon signalling. Furthermore, tuft cells were also observed upon bleomycin injury, suggesting that their development may be a general response to severe lung injury. While intestinal tuft cells promote growth and differentiation of surrounding epithelial cells, in the lungs of tuft cell deficient mice, Krt5+ dysplasia still occurs, goblet cell production is unchanged, and there remains no appreciable contribution of Krt5+ cells into more regionally appropriate alveolar Type 2 cells. Together, these findings highlight unexpected differences in signals necessary for murine lung tuft cell amplification and establish a framework for future elucidation of tuft cell functions in pulmonary health and disease.

Data availability

Sequencing data have been deposited in GEO under accession code GSE197163.In addition to the deposited sequencing data, raw numerical data is available as excel files corresponding to each figure, e.g. Figure 1 - Source Data.xls.

The following data sets were generated

Article and author information

Author details

  1. Justinn Barr

    Department of Pediatrics, University of California, San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Maria Elena Gentile

    Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sunyoung Lee

    Department of Pediatrics, University of California, San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Maya E Kotas

    Division of Pulmonary, Critical Care, Allergy & Sleep Medicine, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Maria Fernanda de Mello Costa

    Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Nicolas P Holcomb

    Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Abigail Jaquish

    Department of Pediatrics, University of California, San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Gargi Palashikar

    Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Marcella Soewignjo

    Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Margaret McDaniel

    Department of Immunology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Ichiro Matsumoto

    Monell Chemical Senses Center, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Robert Margolskee

    Monell Chemical Senses Center, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Jakob Von Moltke

    Department of Immunology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Noam A Cohen

    Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Xin Sun

    Department of Pediatrics, University of California, San Diego, La Jolla, United States
    For correspondence
    xinsun@health.ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8387-4966
  16. Andrew E Vaughan

    Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
    For correspondence
    andrewva@vet.upenn.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5740-643X

Funding

National Institutes of Health (R01HL153539)

  • Andrew E Vaughan

U.S. Department of Veterans Affairs (CX001617)

  • Noam A Cohen

Fonds de Recherche du Québec - Santé

  • Maria Elena Gentile

Lisa Dean Moseley Foundation

  • Andrew E Vaughan

National Institutes of Health (R01HL142215)

  • Xin Sun

National Institutes of Health (1R01AT011676)

  • Xin Sun

National Institutes of Health (T29IR0475)

  • Xin Sun

National Institutes of Health (F32HL151168)

  • Justinn Barr

National Institutes of Health (F32HL140868)

  • Maya E Kotas

National Institutes of Health (T32HL007185)

  • Maya E Kotas

A.P. Giannini Foundation

  • Maya E Kotas

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 (IACUC) of the University of Pennsylvania, the University of California - San Diego, and the University of California, San Francisco. All experiments were performed with every effort to minimize suffering. The protocol number associated with the ethical approval of this work is 806262 (University of Pennsylvania) and S16187 (University of California San Diego).

Reviewing Editor

  1. Paul W Noble, Cedars-Sinai Medical Centre, United States

Publication history

  1. Received: February 22, 2022
  2. Preprint posted: March 11, 2022 (view preprint)
  3. Accepted: September 7, 2022
  4. Accepted Manuscript published: September 8, 2022 (version 1)
  5. Version of Record published: October 11, 2022 (version 2)

Copyright

© 2022, Barr 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

  • 1,140
    Page views
  • 370
    Downloads
  • 2
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Justinn Barr
  2. Maria Elena Gentile
  3. Sunyoung Lee
  4. Maya E Kotas
  5. Maria Fernanda de Mello Costa
  6. Nicolas P Holcomb
  7. Abigail Jaquish
  8. Gargi Palashikar
  9. Marcella Soewignjo
  10. Margaret McDaniel
  11. Ichiro Matsumoto
  12. Robert Margolskee
  13. Jakob Von Moltke
  14. Noam A Cohen
  15. Xin Sun
  16. Andrew E Vaughan
(2022)
Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair
eLife 11:e78074.
https://doi.org/10.7554/eLife.78074

Further reading

    1. Stem Cells and Regenerative Medicine
    Ece Yildiz, Gaby El Alam ... Kristina Schoonjans
    Research Article Updated

    During severe or chronic hepatic injury, biliary epithelial cells (BECs) undergo rapid activation into proliferating progenitors, a crucial step required to establish a regenerative process known as ductular reaction (DR). While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. Here, we demonstrate that BECs readily accumulate lipids during high-fat diet feeding in mice and upon fatty acid treatment in BEC-derived organoids. Lipid overload induces metabolic rewiring to support the conversion of adult cholangiocytes into reactive BECs. Mechanistically, we found that lipid overload activates the E2F transcription factors in BECs, which drive cell cycle progression while promoting glycolytic metabolism. These findings demonstrate that fat overload is sufficient to reprogram BECs into progenitor cells in the early stages of NAFLD and provide new insights into the mechanistic basis of this process, revealing unexpected connections between lipid metabolism, stemness, and regeneration.

    1. Stem Cells and Regenerative Medicine
    Dennis May, Sangwon Yun ... Valentina Greco
    Research Article Updated

    Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline which leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of Keratin-10 (K10) nascent RNA, which marks the onset of stem cell differentiation, we find that Keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.