@article{76b2767125b6460e9f72c15cd104b49c,
title = "Transcriptional Dynamics of Hair-Bundle Morphogenesis Revealed with CellTrails",
abstract = "Protruding from the apical surface of inner ear sensory cells, hair bundles carry out mechanotransduction. Bundle growth involves sequential and overlapping cellular processes, which are concealed within gene expression profiles of individual cells. To dissect such processes, we developed CellTrails, a tool for uncovering, analyzing, and visualizing single-cell gene-expression dynamics. Utilizing quantitative gene-expression data for key bundle proteins from single cells of the developing chick utricle, we reconstructed de novo a bifurcating trajectory that spanned from progenitor cells to mature striolar and extrastriolar hair cells. Extraction and alignment of developmental trails and association of pseudotime with bundle length measurements linked expression dynamics of individual genes with bundle growth stages. Differential trail analysis revealed high-resolution dynamics of transcripts that control striolar and extrastriolar bundle development, including those that encode proteins that regulate [Ca2+]i or mediate crosslinking and lengthening of actin filaments. Ordering single cells along branching trajectories using transcriptomic data is bioinformatically challenging. Ellwanger et al. developed CellTrails and applied this tool to showcase the bifurcating sequence of gene expression as sensory hair cells develop into different subtypes that feature spatially distinct morphologies of the mechanosensitive hair bundle.",
keywords = "clustering, dimensionality reduction, dynamic time warping, hair cell, inner ear, software, spectral embedding, trajectory reconstruction, transcriptomics, vestibular",
author = "Ellwanger, {Daniel C.} and Mirko Scheibinger and Dumont, {Rachel A.} and Barr-Gillespie, {Peter G.} and Stefan Heller",
note = "Funding Information: We thank the Heller laboratory members for inspiring discussions and comments on the manuscript, as well as Dr. D. Maoil?idigh for expert evaluation of mathematical methods, and Drs. Robert Durruthy-Durruthy and Matthew R. Avenarius for their initial help with cell sorting and immunohistochemistry, respectively. P.G.B.-G. is supported by R01DC11034. S.H. is supported by R01DC15201, by the Hearing Health Foundation's Hearing Restoration Project, and through the Stanford Initiative to Cure Hearing Loss by generous gifts from the Evslin family and the Bill and Susan Oberndorf foundations. D.C.E. was supported in part by a Stanford Dean's fellowship. We acknowledge the Stanford Shared FACS facility and the SEM facility at the Center for Electron Microscopy and Nanofabrication, Portland State University. Electron microscopy was also performed at the Multiscale Microscopy Core (MMC) with technical support from the Oregon Health & Science University (OHSU)-FEI Living Lab and the OHSU Center for Spatial Systems Biomedicine. Funding Information: We thank the Heller laboratory members for inspiring discussions and comments on the manuscript, as well as Dr. D. Maoil{\'e}idigh for expert evaluation of mathematical methods, and Drs. Robert Durruthy-Durruthy and Matthew R. Avenarius for their initial help with cell sorting and immunohistochemistry, respectively. P.G.B.-G. is supported by R01DC11034. S.H. is supported by R01DC15201, by the Hearing Health Foundation{\textquoteright}s Hearing Restoration Project , and through the Stanford Initiative to Cure Hearing Loss by generous gifts from the Evslin family and the Bill and Susan Oberndorf foundations . D.C.E. was supported in part by a Stanford Dean{\textquoteright}s fellowship . We acknowledge the Stanford Shared FACS facility and the SEM facility at the Center for Electron Microscopy and Nanofabrication, Portland State University. Electron microscopy was also performed at the Multiscale Microscopy Core (MMC) with technical support from the Oregon Health & Science University (OHSU)-FEI Living Lab and the OHSU Center for Spatial Systems Biomedicine. Publisher Copyright: {\textcopyright} 2018 The Author(s)",
year = "2018",
month = jun,
day = "5",
doi = "10.1016/j.celrep.2018.05.002",
language = "English (US)",
volume = "23",
pages = "2901--2914.e14",
journal = "Cell Reports",
issn = "2211-1247",
publisher = "Cell Press",
number = "10",
}