Mechanisms of stretch-mediated skin expansion at single-cell resolution

Abstract

Data availabilityData associated with this study have been deposited in the NCBI Gene Expression Omnibus under accession numbers GSE126231, GSE126734 and GSE146637 respectively for the microarray, ATAC-seq and single-cell RNA-seq. Data supporting the findings of this study are available within the article (and its Supplementary Information files). Source data behind Figures 1-4 and Extended Data Figures 1-12 are available within the manuscript files. Code availabilityCustom computer code and algorithm used to generate results that are reported in the paper are available within the article (and its Supplementary Information files) and from the corresponding authors on reasonable request. The code used for the modeling of the clonal data has been deposited in GitHub (available at https://github.com/BenSimonsLab/Aragona_Nature_2020). In relation with the single-cells analysis, sequencing reads were preprocessed using cutadapt (version 1.13, https://pypi.org/project/ cutadapt/), alignments were generated using STAR (version 2.5.2b

Gradual differentiation uncoupled from cell cycle exit generates heterogeneity in the epidermal stem cell layer

“…After computational removal of cells from other epithelial compartments (Methods), the combined dataset allowed us to assign the basal-suprabasal border according to the sorted basal (ITGA6+) cells (Figure 2A, Methods). Notably, the previously defined intermediate with recent studies in skin as well as oral epithelia ( Figure S3D) (6,21,22). To more closely examine where the first transcriptional changes begin (signifying the onset of differentiation), we grouped the cells along the trajectory into 10 differentiation bins ( Figure 2D, S3E We found that these divisions occurred parallel to the basement membrane, producing daughter cells that were fully integrated within the basal layer and retained reporter expression ( Figure 3E and Movie S1).…”

“…Extensive efforts have been made to define the cell states and correspondent behaviors within the basal layer that fuel this lifelong tissue turnover. Several studies support a model of epidermal homeostasis through the cooperative efforts of multiple, molecularly distinct progenitor types (Figure S1B) that include fast-cycling, differentiation-primed committed progenitors underpinned by a second, molecularly distinct slow-cycling stem cell population ( 4 , 5 ), pairs of directly coupled stem and differentiation-committed progenitor cells ( 6 ), or two independent stem cell populations with different cycling kinetics and transcriptional profiles ( 7 ). In contrast, other studies instead propose a single type of proliferating progenitor population that generates dividing and differentiating cells with equal probability at the population level ( 8 – 11 ) (Figure S1B) .…”

“…We next aimed to understand how K10 expression relates to the global transcriptional changes associated with basal cell differentiation and to other differentiation-primed progenitor populations that have been described ( 4 – 6 ). Our previous reconstruction of the epidermal differentiation trajectory, based on single-cell transcriptomes of randomly sampled cells from basal and suprabasal layers, grouped the cells according to their individual gene expression from basal ( Krt14 high ), mature ( Krt 10 high ) to terminally differentiated ( Lor high ) cell states ( 20 ).…”

Self-assembling 3D spheroid cultures of human neonatal keratinocytes have enhanced regenerative properties

“…Our findings closely resembled the classic proliferative zone maps of 3D non-scaffold spheroids and the epithelial planarization patterns outlined by several investigators ( Luo et al, 2011 ; Costa et al, 2016 ). This is reminiscent of stretch-induced keratinocyte expansion patterns ( Aragona et al, 2020 ) and reveals that spheroid cultures retain spaciotemporal inclinations that direct cellular fate in culture. It is likely that epidermal stem cells are sensitive to the post-embryonic stage of the tissue of origin.…”

Dia1 Coordinates Differentiation and Cell Sorting in a Stratified Epithelium

“…Disruption of the branched actin nucleator, Arp2/3, or its activator, the WAVE complex, perturbs epidermal function with varying effects on structure (Cohen et al, 2019;van der Kammen et al, 2017;Zhou et al, 2013). Unbranched actin filaments produced by the formin family anchor adhesions and participate in physiological adaptations to mechanical stretch within the epidermis (Aragona et al, 2020;Kobielak et al, 2004). Endogenous miRNA restricts expression of the canonical formin, Dia1, to the basal layer of human epidermis and tongue (Sundaram et al, 2013;Sundaram et al, 2017).…”