22: In depth analyses of non-lesional and lesional atopic dermatitis skin by spatial and single cell sequencing technologies

Mitamura, Yasutaka1; Reiger, Matthias2,3,4; Kim, Juno1; Xiao, Yi1,5; Zhakparov, Damir1,5; Rückert, Beate1; Baerenfaller, Katja1,5; Brüggen, Marie-Charlotte2,6,7; Brunner, Patrick M.8; Roqueiro, Damian9, Traidl-Hoffmann, Claudia2,3,4,10; Akdis, Cezmi A.1,2

  1. Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
  2. CK CARE - Christine Kühne Center for Allergy research and Education, Davos, Switzerland
  3. University of Augsburg, Faculty of Medicine, Department of Environmental Medicine, Augsburg, Germany
  4. Helmholtz Zentrum München, Institute of Environmental Medicine, Augsburg, Germany
  5. Swiss Institute of Bioinformatics (SIB), Davos, Switzerland
  6. University Hospital Zurich, Department of Dermatology, Zurich, Switzerland
  7. University Zurich, Faculty of Medicine, Zurich, Switzerland
  8. Medical University of Vienna, Department of Dermatology, Vienna, Austria
  9. ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
  10. Technical University of Munich, ZIEL, Freising, Germany


Atopic dermatitis (AD) is a chronic inflammatory skin disorder affecting more than 10% of infants and 4% of adults. Because of its huge public health burden, there is a current need to investigate the complex pathogenesis of AD. We and others have performed next-generation RNA sequencing (seq) transcriptome analyses of skin biopsies from AD patients and reported the findings on the immunopathogenesis of AD in the whole RNA. The single-cell analysis of AD lesions showed the details of the molecular and cellular characterization of AD, however the detailed information on spatial and neighboring cells is still not fully understood.


Skin tissues examined for spatial gene expression were derived from the upper arm of 6 healthy control (HC) donors and 7 AD patients (lesion and non-lesion). We performed Visium spatial transcriptomics sequencing (10x Genomics) to characterize the cellular infiltrate in lesional skin. For single-cell analysis, we analyzed the previously published single-cell data from suction blister material from AD lesions and HC skin at the antecubital fossa skin (4 ADs and 5 HCs) and full-thickness skin biopsies (4 ADs and 2 HCs). Both of them were collected and CD45+ cells were enriched by FACS. The multiple proximity extension assays were performed in the serum samples from 29 AD patients and 20 HCs.

Specific aim:

This project aims to investigate the complex pathogenesis of AD with a single-cell and a spatial level to identify molecular mechanisms of skin lesion formation.


The single-cell analysis identified unique clusters of fibroblasts, dendritic cells, macrophages and T cells in the lesional AD skin. Spatial transcriptomics analysis showed the upregulation of COL6A5, COL4A1, TNC, and CCL19 in COL18A1-expressing fibroblasts in the leukocyte-infiltrated areas in AD skin. CCR7-expressing dendritic cells (DCs) were also identified in the lesions. Additionally, M2 macrophages expressed CCL13 and CCL18 in the same localization. Ligand–receptor interaction analysis of the spatial transcriptome identified 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.

Conclusion and impact of this study:

Our results will have a major impact on the dermatologic disease and other allergic diseases because AD initiates the allergic march, such as bronchial asthma, allergic rhinitis, and food allergy. In this study, we report that the leukocyte-infiltrated area in lesional AD skin is characterized by unique inflammatory fibroblasts, M2 macrophages, activated DCs, and T cells interacting with each other and shaping the molecular and cellular characteristics of AD.

Identifying novel mechanisms that play a role in maintaining skin homeostasis and lesion formation can progress in various ways. First, a better understanding of the mechanisms of exacerbations. Second is the demonstration of novel targets for prevention and drug development. Our findings will substantially contribute to decreasing the socioeconomic burden of these devastating diseases.