PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors

  1. Divya Khattar
  2. Sharlene Fernandes
  3. John Snowball
  4. Minzhe Guo
  5. Matthew C Gillen
  6. Suchi Singh Jain
  7. Debora Sinner
  8. William Zacharias
  9. Daniel T Swarr  Is a corresponding author
  1. Cincinnati Children's Hospital Medical Center, United States
  2. Wake Forest University, United States

Abstract

The tips of the developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. Early in embryonic development (prior to E13.5), SOX9+ progenitors are multipotent, generating both airway and alveolar epithelium, but are selective progenitors of alveolar epithelial cells later in development. Transcription factors, including Sox9, Etv5, Irx, Mycn, and Foxp1/2 interact in complex gene regulatory networks to control proliferation and differentiation of SOX9+ progenitors. Molecular mechanisms by which these transcription factors and other signaling pathways control chromatin state to establish and maintain cell-type identity are not well-defined. Herein, we analyze paired gene expression (RNA-Seq) and chromatin accessibility (ATAC-Seq) data from SOX9+ epithelial progenitor cells (EPCs) during embryonic development in Mus musculus. Widespread changes in chromatin accessibility were observed between E11.5 and E16.5, particularly at distal cis-regulatory elements (e.g. enhancers). Gene regulatory network (GRN) inference identified a common SOX9+ progenitor GRN, implicating phosphoinositide 3-kinase (PI3K) signaling in the developmental regulation of SOX9+ progenitor cells. Consistent with this model, conditional ablation of PI3K signaling in the developing lung epithelium in mouse resulted in an expansion of the SOX9+ EPC population and impaired airway epithelial cell differentiation. These data demonstrate that PI3K signaling is required for epithelial patterning during lung organogenesis, and emphasize the combinatorial power of paired RNA and ATAC seq in defining regulatory networks in development.

Data availability

Sequencing data have been deposited in the GEO database, under the accession code GSE188239, GSE188230, and GSE188237.

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

Article and author information

Author details

  1. Divya Khattar

    Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sharlene Fernandes

    Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. John Snowball

    Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Minzhe Guo

    Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Matthew C Gillen

    Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Suchi Singh Jain

    Wake Forest University, Winston-Salem, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Debora Sinner

    Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0704-5223
  8. William Zacharias

    Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2643-0610
  9. Daniel T Swarr

    Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    For correspondence
    Daniel.Swarr@cchmc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7305-0442

Funding

National Institutes of Health (K08HL130666)

  • Daniel T Swarr

National Institutes of Health (K08HL140178)

  • William Zacharias

National Institutes of Health (R01HL144774)

  • Debora Sinner

Cincinnati Children's Hospital Medical Center (Proctor Scholar Award)

  • Daniel T Swarr

National Institutes of Health (5R01HL156860)

  • Daniel T Swarr

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

Ethics

Animal experimentation: 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) protocol (#2019-016) of Cincinnati Children's Hospital Medical Center. The protocol was approved by the Cincinnati Children's Animal Care and Use Committee (Animal Welfare Assurance # A3108-01).

Reviewing Editor

  1. Edward E Morrisey, University of Pennsylvania, United States

Publication history

  1. Preprint posted: February 26, 2021 (view preprint)
  2. Received: February 27, 2021
  3. Accepted: July 14, 2022
  4. Accepted Manuscript published: August 17, 2022 (version 1)
  5. Version of Record published: August 30, 2022 (version 2)

Copyright

© 2022, Khattar 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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  1. Divya Khattar
  2. Sharlene Fernandes
  3. John Snowball
  4. Minzhe Guo
  5. Matthew C Gillen
  6. Suchi Singh Jain
  7. Debora Sinner
  8. William Zacharias
  9. Daniel T Swarr
(2022)
PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors
eLife 11:e67954.
https://doi.org/10.7554/eLife.67954
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