Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis

Abstract

Background: Atopic dermatitis (AD) is a prevalent inflammatory skin disease with a complex pathogenesis involving immune cell and epidermal abnormalities. Despite whole tissue biopsy studies that have advanced the mechanistic understanding of AD, single cell-based molecular alterations are largely unknown. Objective: Our aims were to construct a detailed, high-resolution atlas of cell populations and assess variability in cell composition and cell-specific gene expression in the skin of patients with AD versus in controls. Methods: We performed single-cell RNA sequencing on skin biopsy specimens from 5 patients with AD (4 lesional samples and 5 nonlesional samples) and 7 healthy control subjects, using 103 Genomics. Results: We created transcriptomic profiles for 39,042 AD (lesional and nonlesional) and healthy skin cells. Fibroblasts demonstrated a novel COL6A5 1 COL18A1 1 subpopulation that was unique to lesional AD and expressed CCL2 and CCL19 cytokines. A corresponding LAMP3 1 dendritic cell (DC) population that expressed the CCL19 receptor CCR7 was also unique to AD lesions, illustrating a potential role for fibroblast signaling to immune cells. The lesional AD samples were characterized by expansion of inflammatory DCs (CD1A 1 FCER1A 1) and tissue-resident memory T cells (CD69 1 CD103 1). The frequencies of type 2 (IL13 1)/type 22 (IL22 1) T cells were higher than those of type 1 (IFNG 1) in lesional AD, whereas this ratio was slightly diminished in nonlesional AD and further diminished in controls. Conclusion: AD lesions were characterized by expanded type 2/type 22 T cells and inflammatory DCs, and by a unique inflammatory fibroblast that may interact with immune cells to regulate lymphoid cell organization and type 2 inflammation.

A transcriptomic map of murine and human alopecia areata

“…Both the LC4 skin Langerhans cells and the moDC2 skin CD11b + CCR2 + mDCs, which demonstrated increased relative contributions in AA, had the highest level of expression of MHC-I and MHC-II molecules (Supplemental Figure 2D). Single-cell sequencing in atopic dermatitis has grouped these 2 APC populations and reported a variable increase in lesional versus nonlesional skin (32). Further analysis of subpopulations on DCs and Langerhans cells may reveal a greater role in autoimmune skin conditions.…”

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling

“…UMI counts generated by the ICELL8 3' DE method are unreliable due to residual barcoding primers during cDNA amplification, so we focused on gene detection sensitivity instead. We observed a significant drop in gene detection between the 3' DE and 3' DE-UMI methods (2,849 and 1,288 genes respectively) and a low number of UMIs counted in the 3' DE-UMI method (2,792 UMIs). This suggests that many transcripts are lost in the additional primer digestion and cleanup steps.…”

“…The advent of single-cell RNA-seq has expanded the power to characterize individual immune cells from a defined set of cellsurface markers to the entire transcriptome. These single-cell technologies have enabled immunologists to characterize inflammation [2] and immune responses to cancer [3][4][5][6][7], uncovering previously uncharacterized cellular diversity and cell-type specific transcriptional responses. As recent advances have increased cell throughput and lowered per-cell costs, the number of high-throughput techniques that can process more than a thousand cells per experiment has increased.…”

Cell-Type-Specific Expression of Renin-Angiotensin-System Components in the Human Body and Its Relevance to SARS-CoV-2 Infection

“…For other tissues such as adult lung, esophagus, and spleen published R object containing metadata and raw counts were obtained 5 . We recently published fetal heart 8 , skin 9 , and first-trimester placenta and decidua 10 scRNA-seq data and it was used for generating averaged expression profiles for cell types. Next, we used in-house generated and unpublished scRNA-seq data from tissues of donor and allograft kidney, and testis.…”