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Elife. 2019 Nov 4;8. pii: e50777. doi: 10.7554/eLife.50777.

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

Author information

1
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States.
2
Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States.
3
Genome Analysis Unit, Amgen Research, Amgen Inc, South San Francisco, United States.
4
Oregon Hearing Research Center, Oregon Health & Science University, Portland, United States.
5
Vollum Institute, Oregon Health & Science University, Portland, United States.
6
OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, United States.
7
Graduate School of Dentistry, Kyung Hee University, Seoul, Republic of Korea.
8
Department of Chemistry and Biochemistry, Brigham Young University, Provo, United States.
#
Contributed equally

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.

KEYWORDS:

RNA sequencing; actin; cell biology; chicken; development; developmental biology; hair cells; mass spectrometry; single cells

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