Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq
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 c...
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MDPI AG
2022-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/11/6140 |
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| author | Tu Hu 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 Lone Skov Thomas Litman |
| author_facet | Tu Hu 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 Lone Skov Thomas Litman |
| author_sort | Tu Hu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T01:15:30Z |
| format | Article |
| id | doaj.art-bd531bd745a74000982374ab61df5e31 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T01:15:30Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-bd531bd745a74000982374ab61df5e312023-11-23T14:10:18ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-05-012311614010.3390/ijms23116140Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seqTu Hu0Tanja Todberg1Daniel Andersen2Niels Banhos Danneskiold-Samsøe3Sofie Boesgaard Neestrup Hansen4Karsten Kristiansen5David Adrian Ewald6Susanne Brix7Joel Correa da Rosa8Ilka Hoof9Lone Skov10Thomas Litman11Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, DenmarkDepartment of Dermatology and Allergy, Copenhagen University Hospital—Herlev and Gentofte, 2900 Copenhagen, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, DenmarkDepartment of Biology, University of Copenhagen, 2100 Copenhagen, DenmarkDepartment of Biology, University of Copenhagen, 2100 Copenhagen, DenmarkDepartment of Biology, University of Copenhagen, 2100 Copenhagen, DenmarkBioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, DenmarkLaboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USABioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, DenmarkDepartment of Dermatology and Allergy, Copenhagen University Hospital—Herlev and Gentofte, 2900 Copenhagen, DenmarkBioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, DenmarkTape 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.https://www.mdpi.com/1422-0067/23/11/6140tape strippingatopic dermatitisepidermistranscriptomeBRB-seq |
| spellingShingle | Tu Hu 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 Lone Skov Thomas Litman Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq International Journal of Molecular Sciences tape stripping atopic dermatitis epidermis transcriptome BRB-seq |
| title | Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq |
| title_full | Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq |
| title_fullStr | Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq |
| title_full_unstemmed | Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq |
| title_short | Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq |
| title_sort | profiling the atopic dermatitis epidermal transcriptome by tape stripping and brb seq |
| topic | tape stripping atopic dermatitis epidermis transcriptome BRB-seq |
| url | https://www.mdpi.com/1422-0067/23/11/6140 |
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