Single-cell proteomics reveals changes in expression during hair-cell development

  1. Ying Zhu
  2. Mirko Scheibinger
  3. Daniel Christian Ellwanger
  4. Jocelyn F Krey
  5. Dongseok Choi
  6. Ryan T Kelly
  7. Stefan Heller
  8. Peter G Barr-Gillespie  Is a corresponding author
  1. Pacific Northwest National Laboratory, United States
  2. Stanford University, United States
  3. Oregon Health and Science University, United States
  4. Brigham Young University, United States

Abstract

Hearing and balance rely on small sensory hair cells that reside in the inner ear. To explore dynamic changes in the abundant proteins present in differentiating hair cells, we used nanoliter-scale shotgun mass spectrometry of single cells, each ~1 picoliter, from utricles of embryonic day 15 chickens. We identified unique constellations of proteins or protein groups from presumptive hair cells and from progenitor cells. The single-cell proteomes enabled the de novo reconstruction of a developmental trajectory using protein expression levels, revealing proteins that greatly increased in expression during differentiation of hair cells (e.g., OCM, CRABP1, GPX2, AK1, GSTO1) and those that decreased during differentiation (e.g., TMSB4X, AGR3). Complementary single-cell transcriptome profiling showed corresponding changes in mRNA during maturation of hair cells. Single-cell proteomics data thus can be mined to reveal features of cellular development that may be missed with transcriptomics.

Data availability

The mass spectrometry proteomics data, including raw data from the mass spectrometry runs, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD014256. The analyzed data are reported in Figure 1-source data 1. The analyzed single-cell RNA-seq data are reported in Figure 5-source data 1. The complete analysis of the single-cell RNA-seq will be reported elsewhere

The following data sets were generated

Article and author information

Author details

  1. Ying Zhu

    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States
    Competing interests
    No competing interests declared.
  2. Mirko Scheibinger

    Department of Otolaryngology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  3. Daniel Christian Ellwanger

    Department of Otolaryngology, Stanford University, Stanford, United States
    Competing interests
    Daniel Christian Ellwanger, is affiliated with Amgen Inc.. The author has no other competing interests to declare.
  4. Jocelyn F Krey

    Oregon Hearing Research Center, Oregon Health and Science University, Portland, United States
    Competing interests
    No competing interests declared.
  5. Dongseok Choi

    OHSU-PSU School of Public Health, Oregon Health and Science University, Portland, United States
    Competing interests
    No competing interests declared.
  6. Ryan T Kelly

    Department of Chemistry and Biochemistry, Brigham Young University, Provo, United States
    Competing interests
    No competing interests declared.
  7. Stefan Heller

    Department of Otolaryngology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  8. Peter G Barr-Gillespie

    Oregon Hearing Research Center, Oregon Health and Science University, Portland, United States
    For correspondence
    gillespp@ohsu.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9787-5860

Funding

National Institutes of Health (R01 DC011034)

  • Peter G Barr-Gillespie

National Institutes of Health (R01 DC015201)

  • Stefan Heller

National Institutes of Health (R33 CA225248)

  • Ryan T Kelly

Laboratory Directed Research and Development Program at PNNL (Earth & Biological Sciences Directorate Mission Seed)

  • Ying Zhu

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

Reviewing Editor

  1. Matthew W Kelley, National Institute on Deafness and Other Communication Disorders, United States

Publication history

  1. Received: August 2, 2019
  2. Accepted: November 1, 2019
  3. Accepted Manuscript published: November 4, 2019 (version 1)
  4. Version of Record published: November 14, 2019 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Ying Zhu
  2. Mirko Scheibinger
  3. Daniel Christian Ellwanger
  4. Jocelyn F Krey
  5. Dongseok Choi
  6. Ryan T Kelly
  7. Stefan Heller
  8. Peter G Barr-Gillespie
(2019)
Single-cell proteomics reveals changes in expression during hair-cell development
eLife 8:e50777.
https://doi.org/10.7554/eLife.50777

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