TY - JOUR
T1 - Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq
AU - Hu, Tu
AU - Todberg, Tanja
AU - Andersen, Daniel
AU - Danneskiold-Samsøe, Niels Banhos
AU - Hansen, Sofie Boesgaard Neestrup
AU - Kristiansen, Karsten
AU - Ewald, David Adrian
AU - Brix, Susanne
AU - da Rosa, Joel Correa
AU - Hoof, Ilka
AU - Skov, Lone
AU - Litman, Thomas
N1 - Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/5
Y1 - 2022/5
N2 - 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 tapestripped 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.
AB - 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 tapestripped 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.
KW - atopic dermatitis
KW - BRB-seq
KW - epidermis
KW - tape stripping
KW - transcriptome
UR - http://www.scopus.com/inward/record.url?scp=85131703170&partnerID=8YFLogxK
U2 - 10.3390/ijms23116140
DO - 10.3390/ijms23116140
M3 - Journal article
C2 - 35682818
AN - SCOPUS:85131703170
SN - 1661-6596
VL - 23
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
IS - 11
M1 - 6140
ER -