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Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type-specific immune regulation in atopic dermatitis.

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Updated November 2, 2023

Background Atopic dermatitis (AD) is the most common chronic inflammatory skin disease, but its complex pathogenesis is only insufficiently understood, resulting in still limited treatment options.ObjectiveWe sought to characterize AD on both transcriptomic and proteomic levels in humans.Methods We used skin suction blistering, a painless and nonscarring procedure that can simultaneously sample skin cells and interstitial fluid. We then compared results with conventional biopsies.Results Suction blistering captured epidermal and most immune cells equally well as biopsies, except for mast cells and nonmigratory CD163+ macrophages that were only present in biopsy isolates. Using single-cell RNA sequencing, we found comparable transcriptional profiles of key inflammatory pathways between blister and biopsy AD, but suction blistering was superior in cell-specific resolution for high-abundance transcripts (KRT1/KRT10, KRT16/KRT6A, S100A8/S100A9), which showed some background signals in biopsy isolates. Compared with healthy controls, we found characteristic upregulation of AD-typical cytokines such as IL13 and IL22 in Th2 and Th22 cells, respectively, but we also discovered these mediators in proliferating T cells and natural killer T cells, that also expressed the antimicrobial cytokine IL26. Overall, not T cells, but myeloid cells were most strongly enriched in AD, and we found dendritic cell (CLEC7A, amphiregulin/AREG, EREG) and macrophage products (CCL13) among the top upregulated proteins in AD blister fluid proteomic analyses.ConclusionThese data show that by using cutting-edge technology, suction blistering offers several advantages over conventional biopsies, including better transcriptomic resolution of skin cells, combined with proteomic information from interstitial fluid, unraveling novel inflammatory players that shape the cellular and proteomic microenvironment of AD.

Patrick M BrunnerDepartment of Dermatology, Medical University of Vienna, Vienna, Austriapatrick.brunner@meduniwien.ac.at
Thomas B Rojahn1
Vera Vorstandlechner2
Thomas Krausgruber3
Wolfgang M Bauer1
Natalia Alkon1
Christine Bangert1
Felix M Thaler1
Farzaneh Sadeghyar1
Nikolaus Fortelny3
Victoria Gernedl3
Katharina Rindler1
Adelheid Elbe-Bürger1
Christoph Bock4
Michael Mildner1
Patrick M Brunner5
1Department of Dermatology, Medical University of Vienna, Vienna, Austria.
2Department of Dermatology, Medical University of Vienna, Vienna, Austria; Department of Surgery, Research Laboratory for Thoracic Surgery, Medical University of Vienna, Vienna, Austria.
3CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
4CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
5Department of Dermatology, Medical University of Vienna, Vienna, Austria
Rachel Schwartz

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/1dd552a5-eb4f-4b92-8088-7224bcbd0629
None
GEO Series Accessions:

Atlas

None

Analysis Portals

None

Project Label

SkinAtopicDermatitis10x

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

skin of body

Organ Part

Unspecified

Selected Cell Types

Unspecified

Disease Status (Specimen)

2 disease statuses

Disease Status (Donor)

4 disease statuses

Development Stage

human adult stage

Library Construction Method

2 library construction methods

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_1

File Format

3 file formats

Cell Count Estimate

37.5k

Donor Count

15
mtx.gz15 file(s)tsv.gz30 file(s)xlsx1 file(s)