Single-cell proteomics reveals changes in expression during hair-cell development
- Pacific Northwest National Laboratory, United States
- Stanford University, United States
- Oregon Health and Science University, United States
- 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
Article and author information
Author details
Peter G Barr-Gillespie
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.
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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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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