Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin - PubMed (original) (raw)

. 2023 Jan 31;42(1):111994.

doi: 10.1016/j.celrep.2023.111994. Epub 2023 Jan 24.

Allison C Billi 2, Federico Bocci 3, Ghaidaa Kashgari 4, Enze Xing 2, Lam C Tsoi 5, Leo Meller 4, William R Swindell 6, Rachael Wasikowski 2, Xianying Xing 2, Feiyang Ma 2, Mehrnaz Gharaee-Kermani 7, J Michelle Kahlenberg 7, Paul W Harms 8, Emanual Maverakis 9, Qing Nie 10, Johann E Gudjonsson 11, Bogi Andersen 12

Affiliations

Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin

Julie Wiedemann et al. Cell Rep. 2023.

Abstract

Palmoplantar skin is structurally and functionally unique, but the transcriptional programs driving this specialization are unclear. Here, we use bulk and single-cell RNA sequencing of human palm, sole, and hip skin to describe the distinguishing characteristics of palmoplantar and non-palmoplantar skin while also uncovering differences between palmar and plantar sites. Our approach reveals an altered immune environment in palmoplantar skin, with downregulation of diverse immunological processes and decreased immune cell populations. Further, we identify specific fibroblast populations that appear to orchestrate key differences in cell-cell communication in palm, sole, and hip. Dedicated keratinocyte analysis highlights major differences in basal cell fraction among the three sites and demonstrates the existence of two spinous keratinocyte populations constituting parallel, site-selective epidermal differentiation trajectories. In summary, this deep characterization of highly adapted palmoplantar skin contributes key insights into the fundamental biology of human skin and provides a valuable data resource for further investigation.

Keywords: CP: Cell biology; RNA FISH; epidermal differentation; fibroblast; human epidermis; keratinocyte; palm; palmoplantar skin; single-cell RNA sequencing; skin; sole.

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

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Conflict of interest statement

Declaration of interests J.M.K. has received grant support from Q32 Bio, Celgene/BMS, Ventus Therapeutics, and Janssen. J.M.K. has served on advisory boards for AstraZeneca, Eli Lilly, GlaxoSmithKline, Bristol Myers Squibb, Avion Pharmaceuticals, ProventionBio, Aurinia Pharmaceuticals, Ventus Therapeutics, and Boehringer Ingelheim. J.E.G. has received grant support from Celgene/BMS, Janssen, Eli Lilly, and Almirall. J.E.G. has served on advisory boards for AstraZeneca, Sanofi, Eli Lilly, Boehringer Ingelheim, Novartis, Janssen, Almirall, and BMS.

Figures

Figure 1.

Figure 1.. Bulk RNA sequencing reveals differences between palmoplantar and non-palmoplantar skin

(A) H&E staining of hip, palm, and sole skin. Scale bars: 180 mm (left), 80 mm (right). Black dotted line, dermal-epidermal junction. (B) Principal-component analysis (PCA) plot for 30 samples (15 from hip, 10 from palm, 5 from sole). (C) Heatmap visualizing average expression by site of six gene clusters generated by k-means clustering of the 2,734 differentially expressed genes. (D) Bar plot showing the top five gene ontology (GO) terms for each cluster of genes.

Figure 2.

Figure 2.. Hip, palm, and sole show major differences in cell-type composition

(A) Schematic of sequencing method. Punch biopsies were taken from n = 4 research subjects, with half donating hip and palm and half donating hip and sole. (B) Uniform manifold approximation and projection (UMAP) visualization of all 12 datasets. Each dot represents a single cell (n = 15,243). Colors were determined by unsupervised clustering performed by Seurat. (C) Average expression of three to six well-established gene markers projected onto the UMAP plot to annotate cell types. (D) Heatmap showing the top three most differentially expressed genes for each cluster, as determined by Seurat. Each row represents expression of the marker gene, while each column is an individual cell. (E) Proportion of cell types normalized by the total number of cells in that sequencing type and site. Because of differences in sequencing, proportions of cell types are best compared within conditions.

Figure 3.

Figure 3.. Palmoplantar skin contains a distinct fibroblast population

(A) UMAP visualization of fibroblast subclusters. Each dot represents a single cell (n = 2,303). (B) Proportion of fibroblast subclusters normalized by the total number of cells in that sequencing type. (C) Heatmap of top 10 marker genes for each of the four fibroblast subclusters. (D) CellChat circle plots showing cell-cell communication related to CCL and IGF signaling in the indicated sites.

Figure 4.

Figure 4.. Consistent keratinocyte populations are detected in adult skin

(A) UMAP visualization of keratinocyte subclusters. Each dot represents a single cell (n = 9,801). (B) Average expression of three to six established keratinocyte marker genes projected onto UMAP plots to identify keratinocyte subclusters. (C) Diffusion map of keratinocyte subpopulations. (D) Proportion of cells in each cell-cycle phase (as assigned by the CellCycleScoring function in Seurat) split by site and keratinocyte subcluster. (E) Keratinocyte UMAP colored by cell-cycle phase. (F) Co-immunostaining in the palm skin of proliferation marker Ki67 and differentiation marker KRT1. Inset: arrows indicating suprabasal and basal Ki67-positive cells. White dotted line, dermal-epidermal junction. Scale bar: 60 μm.

Figure 5.

Figure 5.. Notch signaling intensity in keratinocytes differs across hip, palm, and sole

(A) UMAP visualization split up by the three sites (hip, n = 3,845; palm, n = 1,431; sole, n = 4,195), with respective proportions of each cluster. (B) Bar plot showing cell fraction for each site by cluster. Error bars indicate standard deviation. (C) Bar plot showing signaling intensity of Notch signaling in the three sites. (D) Circle plot showing CellChat results for overall Notch signaling in the palm.

Figure 6.

Figure 6.. Adult epidermis contains two distinct spinous populations

(A) Heatmap of top differentially expressed genes between spinous I and spinous II. (B) Heatmap of AUROC scores between keratinocyte clusters based on the highly variable gene set using MetaNeighbor. (C) Feature plot showing the most distinct markers for spinous I and II populations. (D) SCENIC result, with cutoff for AUC score for each transcription factor network (left), UMAP with cells above the given AUC score threshold colored blue (middle), and UMAP with cells colored by the AUC score in red (right). (E) AUCell scoring of GRHL3 network based on Klein et al. Panels as in (D). (F) Bar plot showing specific enrichment of GO terms for spinous I. (G) Bar plot showing specific enrichment of GO terms for spinous II.

Figure 7.

Figure 7.. Spinous populations represent two differentiation trajectories with a shared end state

(A) Monocle pseudotime trajectories showing epidermal differentiation for each site. (B) Violin plots showing distribution of keratinocytes in each cluster over pseudotime for the three sites. (C) Immunostaining of spinous cluster markers GRHL3 and c-FOS in the palm. White dotted line, dermal-epidermal junction. Scale bars: 80 μm. (D) Validation of the presence of two distinct spinous populations by co-immunostaining of GRHL3 and c-FOS in hip and palm skin. White dotted line, dermalepidermal junction. Scale bars: 150 mm.

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