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Schäbitz A, Hillig C, Mubarak M, Jargosch M, Farnoud A, Scala E, Kurzen N, Pilz AC, Bhalla N, Thomas J, Stahle M, Biedermann T, Schmidt-Weber CB, Theis F, Garzorz-Stark N, Eyerich K, Menden MP, Eyerich S. Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases. Nat Commun 2022; 13:7729. [PMID: 36513651 PMCID: PMC9747967 DOI: 10.1038/s41467-022-35319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Abundant heterogeneous immune cells infiltrate lesions in chronic inflammatory diseases and characterization of these cells is needed to distinguish disease-promoting from bystander immune cells. Here, we investigate the landscape of non-communicable inflammatory skin diseases (ncISD) by spatial transcriptomics resulting in a large repository of 62,000 spatially defined human cutaneous transcriptomes from 31 patients. Despite the expected immune cell infiltration, we observe rather low numbers of pathogenic disease promoting cytokine transcripts (IFNG, IL13 and IL17A), i.e. >125 times less compared to the mean expression of all other genes over lesional skin sections. Nevertheless, cytokine expression is limited to lesional skin and presented in a disease-specific pattern. Leveraging a density-based spatial clustering method, we identify specific responder gene signatures in direct proximity of cytokines, and confirm that detected cytokine transcripts initiate amplification cascades of up to thousands of specific responder transcripts forming localized epidermal clusters. Thus, within the abundant and heterogeneous infiltrates of ncISD, only a low number of cytokine transcripts and their translated proteins promote disease by initiating an inflammatory amplification cascade in their local microenvironment.
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Affiliation(s)
- A. Schäbitz
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - C. Hillig
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - M. Mubarak
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - M. Jargosch
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany ,grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - A. Farnoud
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - E. Scala
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ,grid.5963.9Department of Dermatology and Venerology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - N. Kurzen
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - A. C. Pilz
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany ,grid.5963.9Department of Dermatology and Venerology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - N. Bhalla
- grid.5037.10000000121581746Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - J. Thomas
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - M. Stahle
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - T. Biedermann
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - C. B. Schmidt-Weber
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - F. Theis
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - N. Garzorz-Stark
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ,grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - K. Eyerich
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ,grid.5963.9Department of Dermatology and Venerology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.24381.3c0000 0000 9241 5705Department of Dermatology and Venereology, Unit of Dermatology, Karolinska University Hospital, Stockholm, Sweden
| | - M. P. Menden
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany ,grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig-Maximilians University, Goßhadernerstrasse 2, Martinsried, 82152 Germany ,grid.452622.5German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - S. Eyerich
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
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