The Molecular Anatomy of Mouse Skin during Hair Growth and Rest

Skin homeostasis is orchestrated by dozens of cell types that together direct stem cell renewal, lineage commitment, and differentiation. Here, we use single-cell RNA sequencing and single-molecule RNA FISH to provide a systematic molecular atlas of full-thickness skin, determining gene expression profiles and spatial locations that define 56 cell types and states during hair growth and rest. These findings reveal how the outer root sheath (ORS) and inner hair follicle layers coordinate hair production. We found that the ORS is composed of two intermingling but transcriptionally distinct cell types with differing capacities for interactions with stromal cell types. Inner layer cells branch from transcriptionally uncommitted progenitors, and each lineage differentiation passes through an intermediate state. We also provide an online tool to explore this comprehensive skin cell atlas, including epithelial and stromal cells such as fibroblasts, vascular, and immune cells, to spur further discoveries in skin biology. [Display omitted] •Deconstruction of full-thickness skin by single-cell RNA-seq and in situ RNA staining•Basal ORS, suprabasal ORS, companion layer, and LPC cells constitute outer HF layers•Inner HF layers form from unfated progenitors and mature via intermediate states•Fibroblasts spatiotemporally separate into three major subtypes and one cell state Joost et al. use single-cell RNA-seq and in situ mRNA staining to characterize mouse skin during hair growth and rest. 56 identified epithelial and stromal cell populations reveal unprecedented molecular details of cell types and states coordinating hair growth, underlying progenitor commitment and lineage differentiation, spatiotemporal fibroblast heterogeneity, and potential epithelial-stromal interactions.