| Autor: |
Hu T; Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, Denmark.; Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark., Todberg T; Department of Dermatology and Allergy, Copenhagen University Hospital-Herlev and Gentofte, 2900 Copenhagen, Denmark.; Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark., Andersen D; Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark., Danneskiold-Samsøe NB; Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark., Hansen SBN; Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark., Kristiansen K; Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark., Ewald DA; Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, Denmark., Brix S; Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark., Rosa JCD; Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Hoof I; Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, Denmark., Skov L; Department of Dermatology and Allergy, Copenhagen University Hospital-Herlev and Gentofte, 2900 Copenhagen, Denmark.; Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark., Litman T; Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, Denmark.; Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark. |
| Abstrakt: |
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. |
