1. Developmental Biology
  2. Stem Cells and Regenerative Medicine

Single-cell transcriptomics of a dynamic cell behavior in murine airways

  1. Sheldon JJ Kwok
  2. Daniel T Montoro
  3. Adam L Haber
  4. Seok-Hyun Yun  Is a corresponding author
  5. Vladimir Vinarsky  Is a corresponding author
  1. LASE Innovation Inc, United States
  2. Broad Institute, United States
  3. Harvard Medical School, United States
  4. Massachusetts General Hospital, United States
https://doi.org/10.7554/eLife.76645
Share this article
Cite this article
  1. Sheldon JJ Kwok
  2. Daniel T Montoro
  3. Adam L Haber
  4. Seok-Hyun Yun
  5. Vladimir Vinarsky
(2023)
Single-cell transcriptomics of a dynamic cell behavior in murine airways
eLife 12:e76645.
https://doi.org/10.7554/eLife.76645
  2. Download BibTeX
  3. Download .RIS

Abstract

Despite advances in high-dimensional cellular analysis, the molecular profiling of dynamic behaviors of cells in their native environment remains a major challenge. We present a method that allows us to couple physiological behaviors of cells in an intact murine tissue to deep molecular profiling of individual cells. This method enabled us to establish a novel molecular signature for a striking migratory cellular behavior following injury in murine airways.

Data availability

Sequencing data have been deposited in GEO under accession code GSE193954.

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

Article and author information

Author details

  1. Sheldon JJ Kwok

    LASE Innovation Inc, Cambridge, United States
    Competing interests
    Sheldon JJ Kwok, Currently an employee of and has financial interests in LASE Innovation Inc..

  2. Daniel T Montoro

    Broad Institute, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6222-2149

  3. Adam L Haber

    Broad Institute, Cambridge, United States
    Competing interests
    No competing interests declared.

  4. Seok-Hyun Yun

    Wellman Center for Photomedicine, Harvard Medical School, Cambridge, United States
    For correspondence
    seok-hyun_yun@hms.harvard.edu
    Competing interests
    Seok-Hyun Yun, Has financial interests in LASE Innovation Inc. that were reviewed and are managed by Massachusetts General Hospital and Mass General Brigham in accordance with their conflict-of-interest policies..

  5. Vladimir Vinarsky

    Center for Regenerative Medicine, Massachusetts General Hospital, Boston, United States
    For correspondence
    vvinarsky@gmail.com
    Competing interests
    Vladimir Vinarsky, Currently an employee and has financial interest in Vertex Pharmaceuticals, Inc..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1141-6434

Funding

National Heart, Lung, and Blood Institute (5P01HL120839)

  • Seok-Hyun Yun

National Heart, Lung, and Blood Institute (5F32HL154638)

  • Daniel T Montoro

National Institute of Biomedical Imaging and Bioengineering (P41EB015903)

  • Seok-Hyun Yun

National Institute of Biomedical Imaging and Bioengineering (P41EB015903)

  • Seok-Hyun Yun

National Cancer Institute (R01CA192878)

  • Seok-Hyun Yun

National Heart, Lung, and Blood Institute (K08HL124298)

  • Vladimir Vinarsky

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

Reviewing Editor

  1. Murim Choi, Seoul National University, Republic of Korea

Ethics

Animal experimentation: Mice were maintained in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited animal facility at the Massachusetts General Hospital, and procedures were performed with Institutional Animal Care and Use Committee (IACUC)-approved protocol 2009N000119.

Version history

  1. Received: December 23, 2021
  2. Preprint posted: January 31, 2022 (view preprint)
  3. Accepted: April 20, 2023
  4. Accepted Manuscript published: April 21, 2023 (version 1)
  5. Version of Record published: May 11, 2023 (version 2)

Copyright

© 2023, Kwok 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

  • 1,643
    views
  • 177
    downloads
  • 1
    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. Sheldon JJ Kwok
  2. Daniel T Montoro
  3. Adam L Haber
  4. Seok-Hyun Yun
  5. Vladimir Vinarsky
(2023)
Single-cell transcriptomics of a dynamic cell behavior in murine airways
eLife 12:e76645.
https://doi.org/10.7554/eLife.76645

Share this article

https://doi.org/10.7554/eLife.76645

Categories and tags

Research organism

Further reading

    1. Developmental Biology

    Inhibitory G proteins play multiple roles to polarize sensory hair cell morphogenesis

    Amandine Jarysta, Abigail LD Tadenev ... Basile Tarchini
    Research Article

    Inhibitory G alpha (GNAI or Gαi) proteins are critical for the polarized morphogenesis of sensory hair cells and for hearing. The extent and nature of their actual contributions remains unclear, however, as previous studies did not investigate all GNAI proteins and included non-physiological approaches. Pertussis toxin can downregulate functionally redundant GNAI1, GNAI2, GNAI3, and GNAO proteins, but may also induce unrelated defects. Here, we directly and systematically determine the role(s) of each individual GNAI protein in mouse auditory hair cells. GNAI2 and GNAI3 are similarly polarized at the hair cell apex with their binding partner G protein signaling modulator 2 (GPSM2), whereas GNAI1 and GNAO are not detected. In Gnai3 mutants, GNAI2 progressively fails to fully occupy the sub-cellular compartments where GNAI3 is missing. In contrast, GNAI3 can fully compensate for the loss of GNAI2 and is essential for hair bundle morphogenesis and auditory function. Simultaneous inactivation of Gnai2 and Gnai3 recapitulates for the first time two distinct types of defects only observed so far with pertussis toxin: (1) a delay or failure of the basal body to migrate off-center in prospective hair cells, and (2) a reversal in the orientation of some hair cell types. We conclude that GNAI proteins are critical for hair cells to break planar symmetry and to orient properly before GNAI2/3 regulate hair bundle morphogenesis with GPSM2.

    1. Computational and Systems Biology
    2. Developmental Biology

    A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

    Gang Xue, Xiaoyi Zhang ... Zhiyuan Li
    Research Article

    Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding question in this field is how these tangled interactions synergistically contribute to decision-making procedures. To comprehensively understand the role of regulatory logic in cell fate decisions, we constructed a logic-incorporated GRN model and examined its behavior under two distinct driving forces (noise-driven and signal-driven). Under the noise-driven mode, we distilled the relationship among fate bias, regulatory logic, and noise profile. Under the signal-driven mode, we bridged regulatory logic and progression-accuracy trade-off, and uncovered distinctive trajectories of reprogramming influenced by logic motifs. In differentiation, we characterized a special logic-dependent priming stage by the solution landscape. Finally, we applied our findings to decipher three biological instances: hematopoiesis, embryogenesis, and trans-differentiation. Orthogonal to the classical analysis of expression profile, we harnessed noise patterns to construct the GRN corresponding to fate transition. Our work presents a generalizable framework for top-down fate-decision studies and a practical approach to the taxonomy of cell fate decisions.

    1. Developmental Biology
    2. Evolutionary Biology

    The rapidly evolving X-linked MIR-506 family fine-tunes spermatogenesis to enhance sperm competition

    Zhuqing Wang, Yue Wang ... Wei Yan
    Research Article

    Despite rapid evolution across eutherian mammals, the X-linked MIR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (SLITRK2 and FMR1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked MIR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernible defects, but simultaneous ablation of five clusters containing 19 members of the MIR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility, and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked MIR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the MIR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.