TY - JOUR T1 - Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics JF - bioRxiv DO - 10.1101/793117 SP - 793117 AU - Daniel Haensel AU - Suoqin Jin AU - Rachel Cinco AU - Peng Sun AU - Quy Nguyen AU - Zixuan Cang AU - Morgan Dragan AU - Yanwen Gong AU - Adam L MacLean AU - Kai Kessenbrock AU - Enrico Gratton AU - Qing Nie AU - Xing Dai Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/10/04/793117.abstract N2 - Our knowledge of transcriptional heterogeneities in epithelial stem/progenitor cell compartments is limited. Epidermal basal cells sustain cutaneous tissue maintenance and drive wound healing. Previous studies have probed basal cell heterogeneity in stem/progenitor potential, but a non-biased dissection of basal cell dynamics during differentiation is lacking. Using single-cell RNA-sequencing coupled with RNAScope and fluorescence lifetime imaging, we identify three non-proliferative and one proliferative basal cell transcriptional states in homeostatic skin that differ in metabolic preference and become spatially partitioned during wound re-epithelialization. Pseudotemporal trajectory and RNA velocity analyses produce a quasi-linear differentiation hierarchy where basal cells progress from Col17a1high/Trp63high state to early response state, proliferate at the juncture of these two states, or become growth arrested before differentiating into spinous cells. Wound healing induces plasticity manifested by dynamic basal-spinous interconversions at multiple basal states. Our study provides a systematic view of epidermal cellular dynamics supporting a revised “hierarchical-lineage” model of homeostasis.Bulge hair follicle stem cells(Bu-HFSCs)Canonical Correlation Analysis(CCA)Dendritic cell(DC)Early response(ER)Epithelial-to-mesenchymal transition(EMT)Fluorescence lifetime imaging microscopy(FLIM)Gaussian process regression(GPR)Gene ontology(GO)Growth arrested(GA)Hair follicle(HF)Label-retaining cell(LRC)Single cell RNA-sequencing(scRNA-Seq)t-distributed stochastic neighbor embedding (tSNE) Transcription factor(TF)Two-photon excitation(TPE)Uniform manifold approximation and projection(UMAP)Un-wounded(UW)Wounded(WO) ER -