Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA614539: Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis

Source: NCBI / GSE147424
Submission Date: Mar 23 2020
Release Date: Mar 24 2020
Update Date: Mar 26 2020

Summary: 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: To construct a detailed, high-resolution atlas of cell populations, and to assess variability in cell composition and cell-specific gene expression in the skin of AD patients versus controls. Methods: We performed single-cell RNA-sequencing on skin biopsies from 5 patients with AD (4 lesional samples, 5 non-lesional samples) and 7 healthy control subjects, using 10x Genomics. Results: We created transcriptomic profiles for 39,042 AD (lesional and non-lesional) and healthy skin cells. Fibroblasts demonstrated a novel COL6A5+COL18A1+ subpopulation that was unique to lesional AD, and expressed CCL2 and CCL19 cytokines. A corresponding LAMP3+ 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. Lesional AD samples were characterized by expansion of inflammatory DCs (CD1A+FCER1A+) and tissue resident memory T-cells (CD69+CD103+). The frequencies of type 2 (IL13+)/type 22 (IL22+) T-cells were higher than type 1 (IFNG+) in lesional AD, while this ratio was diminished slightly in non-lesional AD and further in controls. Conclusion: AD lesions were characterized by expanded type 2/type 22 T-cells and inflammatory DCs, and a unique inflammatory fibroblast that may interact with immune cells to regulate lymphoid cell organization and type 2 inflammation.

Overall Design: Lesional/non-lesional skin biopsies were taken from the extremities of 5 moderate-to-severe AD patients and 7 matching controls. Biopsies were cryopreserved and processed by 10x Genomics. The library was sequenced on the Illumina HiSeq 2500 platform.

GEN Datasets:
GEND000109
Strategy:
Species:
Tissue:
Healthy Condition:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Cryopreserved skin biopsies were thawed, dissociated in a Liberase solution twice, and then dissociated again in a Trypsin solution. The tissues were subsequently re-suspended in PBS-bovine serum albumin.
Library Construction Protocol: The Chromium Single Cell 3' Reagent Kit V2 (10x Genomics) was used to generate single-cell libraries, according to manufacturer instructions. The library was sequenced on the Illumina HiSeq 2500 platform.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Publications
Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis.
The Journal of allergy and clinical immunology . 2020-02-07 [PMID: 32035984]