How stem cells give rise to human interfollicular epidermis is unclear despite the crucial role the epidermis plays in barrier and appendage formation. Here we use single cell-RNA sequencing to interrogate basal stem cell heterogeneity of human interfollicular epidermis and find at least four spatially distinct stem cell populations that decorate the top and bottom of rete ridge architecture and hold transitional positions between the basal and suprabasal epidermal layers. Cell-cell communication modeling through co-variance of cognate ligand-receptor pairs indicate that the basal cell populations distinctly serve as critical signaling hubs that maintain epidermal communication. Combining pseudotime, RNA velocity, and cellular entropy analyses point to a hierarchical differentiation lineage supporting multi-stem cell interfollicular epidermal homeostasis models and suggest the "transitional" basal stem cells are stable states essential for proper stratification. Finally, alterations in differentially expressed "transitional" basal stem cell genes result in severe thinning of human skin equivalents, validating their essential role in epidermal homeostasis and reinforcing the critical nature of basal stem cell heterogeneity. Joost et al., 2018). Despite these studies, epidermal stem cell heterogeneity of human IFE remains unresolved. To address this issue, we interrogated epidermal cell heterogeneity within human neonatal foreskin epidermis using droplet-enabled scRNA-seq and identify four spatially distinct basal stem cell subpopulations. Interrogation of the "transitional" basal subpopulations that spatially occupy both the basal and suprabasal layers indicate their essential role in epidermal homeostasis. Our findings argue against a single population of progenitor cells and suggest a more complex model of multiple epidermal stem cell transitions that maintain epidermal homeostasis.
RESULTS
Single cell transcriptome analysis reveals robust cellular heterogeneity in human neonatal
epidermis.To define the cellular heterogeneity of human IFE, we isolated viable, single cells from discarded and de-identified human neonatal foreskin epidermis and subjected them to droplet-enabled scRNA-seq to resolve their individual transcriptomes ( Figure 1A; Supplementary Figure 1; Supplementary Table 1; n = 5). We chose foreskin epidermis because it is composed of mostly IFE and contains few rudimentary skin appendages, such as hair follicles and sweat glands (Tuncali et al., 2005). We processed a total of 17,553 cells and performed quality control analysis on individual libraries using Seurat (Supplementary Figure 2) (Macosko et al., 2015). We used Similarity matrix-based OPtimization for Single Cell (SoptSC) to bioinformatically parse and analyze our data . The SoptSC algorithm is based on a cell-cell similarity matrix that can coherently perform many inference tasks -including unsupervised clustering, pseudotemporal ordering, cell lineage inference, cell-cell communication, and network inference.We used library three as a repr...