Spatial transcriptomics combined with single-cell RNA-sequencing unravels the complex inflammatory cell network in atopic dermatitis [ST]
Dataset ID: STDS0000212


Dataset information
Atopic dermatitis (AD) is the most common chronic inflammatory skin disease with complex pathogenesis. Using spatial and single-cell transcriptomics of whole skin biopsy and suction blister material, we investigated the cellular and molecular features of the leukocyte-infiltrated area in AD. We identified unique clusters of fibroblasts, dendritic cells, macrophages, and T cells in the lesional AD skin and molecular interactions between these cells. The leukocyte-infiltrated areas in lesional AD skin showed upregulation of COL6A5, COL4A1, TNC, IL32, CCL19 in COL18A1-expressing fibroblasts. Additionally, M2 macrophages expressed CCL13 and CCL18 in the same localization. Ligand–receptor interaction analysis of the spatial transcriptome identified a neighboring infiltration and interaction between activated COL18A1-expressing fibroblasts, activated CCL13- and CCL18-expressing M2 macrophages, CCR7- and LAMP3-expressing DCs, and T cells. As observed in skin lesions, serum levels of TNC and CCL18 were significantly elevated in AD and correlated with clinical disease severity.
Overall design:
Spatial Transcriptomics (Visium Spatial Gene Expression; 10X Genomics) of human skin biopsy samples. 14 skin biopsy samples were collected from 7 atopic dermatitis patients, 1 from lesional and 1 from non-lesional skin per patient. In addition, 6 skin biopsy samples were collected from 6 healthy donors to serve as a control.
10x Visium
Illumina NovaSeq 6000
Homo sapiens(hg38)
Organ parts:
Atopic dermatitis lesional skin, Atopic dermatitis non-lesional skin, Skin
Atopic dermatitis | Healthy
Mitamura, Yasutaka et al. “Spatial transcriptomics combined with single-cell RNA-sequencing unravels the complex inflammatory cell network in atopic dermatitis.” Allergy vol. 78,8 (2023): 2215-2231. doi:10.1111/all.15781
Submission date: 2022-02-18Update date: 2023-08-11
Sample number: 20Section number: 20

Mitamura, Yasutaka; Reiger, Matthias; Kim, Juno; Xiao, Yi; Zhakparov, Damir; Tan, Ge; Rinaldi, Arturo O; Baerenfaller, Katja; Akdis, Mübeccel; Brüggen, Marie-Charlotte; Brunner, Patrick M; Roqueiro, Damian; Traidl-Hoffmann, Claudia; Akdis, Cezmi A

GEO Series Accessions: GSE197023