Single-cell proteomics reveals changes in expression during hair-cell development
Ying Zhu,
Mirko Scheibinger,
Daniel Christian Ellwanger,
Jocelyn F Krey,
Dongseok Choi,
Ryan T Kelly,
Stefan Heller,
Peter G Barr-Gillespie
Affiliations
Ying Zhu
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States
Mirko Scheibinger
Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States
Daniel Christian Ellwanger
Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States; Genome Analysis Unit, Amgen Research, Amgen Inc, South San Francisco, United States
Jocelyn F Krey
Oregon Hearing Research Center, Oregon Health & Science University, Portland, United States; Vollum Institute, Oregon Health & Science University, Portland, United States
Dongseok Choi
OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, United States; Graduate School of Dentistry, Kyung Hee University, Seoul, Republic of Korea
Ryan T Kelly
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States; Department of Chemistry and Biochemistry, Brigham Young University, Provo, United States
Stefan Heller
Department of Otolaryngology Head and Neck Surgery, Stanford University, Stanford, United States
Oregon Hearing Research Center, Oregon Health & Science University, Portland, United States; Vollum Institute, Oregon Health & Science University, Portland, United States
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.
