Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

Abstract

SummaryThe murine epidermis with its hair follicles represents an invaluable model system for tissue regeneration and stem cell research. Here we used single-cell RNA-sequencing to reveal how cellular heterogeneity of murine telogen epidermis is tuned at the transcriptional level. Unbiased clustering of 1,422 single-cell transcriptomes revealed 25 distinct populations of interfollicular and follicular epidermal cells. Our data allowed the reconstruction of gene expression programs during epidermal differentiation and along the proximal-distal axis of the hair follicle at unprecedented resolution. Moreover, transcriptional heterogeneity of the epidermis can essentially be explained along these two axes, and we show that heterogeneity in stem cell compartments generally reflects this model: stem cell populations are segregated by spatial signatures but share a common basal-epidermal gene module. This study provides an unbiased and systematic view of transcriptional organization of adult epidermis and highlights how cellular heterogeneity can be orchestrated in vivo to assure tissue homeostasis.

Skin and Its Regenerative Powers: An Alliance between Stem Cells and Their Niche

“…Cells along the basement membrane in the outer bulge layer display traits often associated with long-term stem cell populations, including (1) their ability to give rise to all lineages of the regenerating lower HF when traced either by dilution of H2BGFP fluorescence, or by K15-CrePGR or Lgr5-CreER , both of which mark the lower bulge and HG (Morris et al, 2004; Nowak et al, 2008; Tumbar et al, 2004); (2) their clonogenic nature when cultured in vitro (Blanpain et al, 2004; Claudinot et al, 2005); and (3) their versatility upon transplantation; they are able to regenerate epidermis, SGs, and cycling HFs that are replete with their own HFSC niche (Blanpain et al, 2004; Oshima et al, 2001). By single-cell RNA-sequencing, bulge HFSCs were found to be homogeneous and high in their levels of integrins α3β1 and α6β4, KRT5/14, LGR5, SOX9, TCF3/4, NFATc1, and LHX2 (Joost et al, 2016; Yang et al, 2017). …”

Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis

“…Firstly, we calculated the proportion of E7 positive cells in each cluster and observed the highest proportions were in clusters classified as basal keratinocytes (54.4%), including those in the HF outer bulge, with a significantly smaller proportion in differentiated keratinocytes (19.6%; p=3.29x10 -34 ). When we compared the top marker genes of between each of the cell types, we found that E7 was one of the top genes representing the basal keratinocytes of the HF outer bulge, classified by Cd34/Postn/Krt5/Krt14 expression (Joost et al, 2016). This finding is reminiscent of HPV DNA detection in hair follicles of eyebrows and those in the vicinity of genital warts (Boxman et al, 1999, Neale et al, 2013, Poljak et al, 2009).…”

“…A recent study of mouse hair follicle (HF) and epidermis (Joost et al, 2016) established robust genetic markers associated with specific cell subtypes. To better understand the cellular heterogeneity of the C57BL/6 and K14E7 mouse epidermis, scRNA-seq data of cells from both animal strains were combined and dissected using the unbiased, graph-based clustering method (Waltman and van Eck, 2013) implemented in Seurat ( Figure 2B), revealing 14 distinct clusters ( Figure 2C).…”

“…To better understand the cellular heterogeneity of the C57BL/6 and K14E7 mouse epidermis, scRNA-seq data of cells from both animal strains were combined and dissected using the unbiased, graph-based clustering method (Waltman and van Eck, 2013) implemented in Seurat ( Figure 2B), revealing 14 distinct clusters ( Figure 2C). Cell type identifiers were assigned using marker genes (Joost et al, 2016) ( Figure 2D; Figure S1; Table S3-S4). Several cell types were shared between the C57BL/6 and K14E7 mice, but each strain also contained its own discrete populations of keratinocytes ( Figure 2C).…”

Inhibition of β-Catenin Signaling in the Skin Rescues Cutaneous Adipogenesis in Systemic Sclerosis: A Randomized, Double-Blind, Placebo-Controlled Trial of C-82

“…Genes showing increased expression in C-82-treated skin include both proteins coating lipid droplets and proteins involved in synthesizing lipid components of lipid droplets (Table 3, (D’Aquila et al, 2015, Kimmel and Sztalryd, 2016, Schneider et al, 2016)). Sebocyte-regulated genes were particularly well represented, possibly because we were able to identify gene expressed by these cells using data from a recent single cell RNA-seq experiment (Joost et al, 2016)).…”