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

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PMID: 37312623
Summary
Visualization
Data
Analysis results
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Dataset information
Summary:
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.
Technology:
10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Homo sapiens(hg38)
Tissues:
Skin
Organ parts:
Atopic dermatitis lesional skin,Atopic dermatitis non-lesional skin,Skin
Disease:
Atopic dermatitis | Healthy
Submission date: 2022-02-18Update date: 2023-08-11
Sample number: 20Section number: 20
DOI: To be continue
Contributors
Mitamura, Yasutaka,Reiger, Matthias,Kim, Juno,Xiao, Yi,Zhakparov, Damir,Tan, Ge,Rinaldi, Arturo O,Ba
Accessions
GEO Series Accessions: GSE197023
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Mitamura, Yasutaka,Reiger, Matthias,Kim, Juno,Xiao, Yi,Zhakparov, Damir,Tan, Ge,Rinaldi, Arturo O,Ba. Spatial transcriptomics combined with single-cell RNA-sequencing unravels the complex inflammatory cell network in atopic dermatitis [ST][DS/OL]. STOmicsDB, 2022[2022-02-18]. https://db.cngb.org/stomics/datasets/STDS0000212/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: 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