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Article

Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq

by
Tu Hu
1,2,
Tanja Todberg
3,4,
Daniel Andersen
5,
Niels Banhos Danneskiold-Samsøe
6,
Sofie Boesgaard Neestrup Hansen
6,
Karsten Kristiansen
6,
David Adrian Ewald
1,
Susanne Brix
5,
Joel Correa da Rosa
7,
Ilka Hoof
1,
Lone Skov
3,4 and
Thomas Litman
1,2,*
1
Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, Denmark
2
Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
3
Department of Dermatology and Allergy, Copenhagen University Hospital—Herlev and Gentofte, 2900 Copenhagen, Denmark
4
Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
5
Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark
6
Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
7
Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2022, 23(11), 6140; https://doi.org/10.3390/ijms23116140
Submission received: 24 March 2022 / Revised: 12 May 2022 / Accepted: 25 May 2022 / Published: 30 May 2022
(This article belongs to the Special Issue Molecular Research on Inflammatory Skin Diseases)
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Abstract

Tape stripping is a non-invasive skin sampling technique, which has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated immune response. Here, we performed BRB-seq—a low cost, multiplex-based, transcriptomic profiling technique—on tape-stripped skin from 30 AD patients and 30 healthy controls to evaluate the methods’ ability to assess the epidermal AD transcriptome. An AD signature consisting of 91 differentially expressed genes, specific for skin barrier and inflammatory response, was identified. The gene expression in the outermost layers, stratum corneum and stratum granulosum, of the skin showed highest correlation between tape-stripped skin and matched full-thickness punch biopsies. However, we observed that low and highly variable transcript counts, probably due to low RNA yield and RNA degradation in the tape-stripped skin samples, were a limiting factor for epidermal transcriptome profiling as compared to punch biopsies. We conclude that deep BRB-seq of tape-stripped skin is needed to counteract large between-sample RNA yield variation and highly zero-inflated data in order to apply this protocol for population-wide screening of the epidermal transcriptome in inflammatory skin diseases.
Keywords: tape stripping; atopic dermatitis; epidermis; transcriptome; BRB-seq tape stripping; atopic dermatitis; epidermis; transcriptome; BRB-seq

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MDPI and ACS Style

Hu, T.; Todberg, T.; Andersen, D.; Danneskiold-Samsøe, N.B.; Hansen, S.B.N.; Kristiansen, K.; Ewald, D.A.; Brix, S.; Rosa, J.C.d.; Hoof, I.; et al. Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq. Int. J. Mol. Sci. 2022, 23, 6140. https://doi.org/10.3390/ijms23116140

AMA Style

Hu T, Todberg T, Andersen D, Danneskiold-Samsøe NB, Hansen SBN, Kristiansen K, Ewald DA, Brix S, Rosa JCd, Hoof I, et al. Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq. International Journal of Molecular Sciences. 2022; 23(11):6140. https://doi.org/10.3390/ijms23116140

Chicago/Turabian Style

Hu, Tu, Tanja Todberg, Daniel Andersen, Niels Banhos Danneskiold-Samsøe, Sofie Boesgaard Neestrup Hansen, Karsten Kristiansen, David Adrian Ewald, Susanne Brix, Joel Correa da Rosa, Ilka Hoof, and et al. 2022. "Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq" International Journal of Molecular Sciences 23, no. 11: 6140. https://doi.org/10.3390/ijms23116140

APA Style

Hu, T., Todberg, T., Andersen, D., Danneskiold-Samsøe, N. B., Hansen, S. B. N., Kristiansen, K., Ewald, D. A., Brix, S., Rosa, J. C. d., Hoof, I., Skov, L., & Litman, T. (2022). Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq. International Journal of Molecular Sciences, 23(11), 6140. https://doi.org/10.3390/ijms23116140

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