Profilig the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA818188 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18396200.fastq.gz | Fastqsanger.gz | |||
| SRR18396300.fastq.gz | Fastqsanger.gz | |||
| SRR18396201.fastq.gz | Fastqsanger.gz | |||
| SRR18396301.fastq.gz | Fastqsanger.gz | |||
| SRR18396202.fastq.gz | Fastqsanger.gz |
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Project description:Tape stripping 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) to study the epidermal transcriptome of AD patients and healthy controls from tape stripped skin samples.
2022-05-31 | GSE199046 | GEO
Project description:Background: Skin biopsies represent a gold standard in skin immunology and pathology but can cause pain and induce scarring. Non-invasive techniques will facilitate study recruitment of e.g. patients with pediatric atopic dermatitis (AD), hand eczema or facial dermatitis. Objective: By RNA sequencing, we examined whether the stratum corneum transcriptome in AD skin can be assessed by tape stripping, as compared to the epidermal transcriptome of AD in skin biopsies. To make the procedure clinically relevant tape strips were stored and shipped at room temperature for up to 3 days. Methods: Nine adult Caucasian AD patients and three healthy volunteers were included. Tape samples were collected from non-lesional and lesional skin. Biopsies were collected from lesional skin and were split into epidermis and dermis. Total RNA was extracted, and shotgun sequencing was performed. Results: Shotgun sequencing could be performed on skin cells obtained from two consecutive tape strips which had been stored and shipped at room temperature for up to three days. The most prominent differences between the tape strip and biopsy derived transcriptome were due to structural genes, while established molecular markers of AD, including CCL17, CCL22, IL17A and S100A7-S100A9, were also identified in tape strip samples. Furthermore, the tape strip derived transcriptome showed promise in also analysing the skin microbiome. Conclusion: Our study shows that the stratum corneum (SC) transcriptome of AD can be assessed by tape stripping the skin, supporting that this method may be central in future skin biomarker research.
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Project description:The stratum corneum transcriptome in atopic dermatitis can be assessed by tape stripping
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Project 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.
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Project description:The objective of this study was to provide a comprehensive evaluation of how well tape-stripping paired with high resolution RNA-sequencing captures the global transcriptomic changes in psoriasis.
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Project description:Use of tape stripping for the collection of stratum corneum is a versatile and reliable procedure for the evaluation of the human skin health, including assessments of the skin barrier function, microbial content, and disease biomarkers. The tape stripping procedure is widely referenced; however, the number and type of tapes required for sample collection vary considerably, and the lack of standardized sampling, processing and normalization protocols complicate data comparison and interpretation. We have compared the performances of two commonly used non-invasive skin sampling platforms by collecting skin tissue from 34 healthy volunteers and applying standardization throughout the workflow, from sampling to data analysis. Our results showed significant differences in the amounts of tissue collected per tape, erythema levels, RNA and protein yields. RNA extracts from both platforms were suitable for sequencing; comparable input and quality of reads were produced for both test groups, however significant differences were found in the percentage of uniquely mapped reads and detected genes. This data highlights processing optimization as an important step in maximizing the efficiency of biomolecule extraction from tape strips and further presents a tape stripping method suitable for fast, efficient, and non-invasive epidermal tissue collection applicable to skin biomarker discovery.
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Project description:Hand eczema (HE) is a prevalent skin disease. However, classification of HE into different subtypes remains challenging. Limited number of prior studies have employed invasive biopsy-based strategies; yet, studies of the HE proteome using non-invasive tape stripping methodology have not been reported. In this study, we wanted to assess whether global proteomic analysis of skin tape strip samples can be used for sub-classification of HE patients. Tape strips were collected from patients with HE and healthy skin. Liquid chromatography–mass spectrometry (LC/MS) proteomics was performed, and the global protein expression was analyzed. We identified 2,919 proteins in stratum corneum-derived skin cells from tape strip samples. Compared to healthy skin, the lesional samples from HE patients exhibited increased expression of immune-related markers and a decreased expression of structural barrier proteins. The difference between HE subtypes was restricted to the lesional skin areas, and included an increased expression of skin barrier-related proteins independently of the concurrent AD. In conclusion we found, that the non-invasive tape strip method used in combination with LC/MS proteomics can be used for analysis of skin protein expression in HE patients. Thus, the method shows potential for assessing the proteomic differences between subtypes of HE, and biomarker discovery.
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Project description:Clinical overlaps between psoriasis and atopic dermatitis are sometimes undiscernible, and there is no consensus whether to treat the overlap phenotype as psoriasis or atopic dermatitis. We enrolled patients diagnosed with either psoriasis or atopic dermatitis, and clinically re-stratified them into classic psoriasis, classic atopic dermatitis, and the overlap phenotype between psoriasis and atopic dermatitis. We compared gene expression profiles of lesional and nonlesional skin biopsy tissues between the three comparison groups. Global mRNA expression and T-cell subset cytokine expression in the skin of the overlap phenotype were consistent with the profiles of psoriasis and different from the profiles of atopic dermatitis. Unsupervised k-means clustering indicated that the best number of distinct clusters for the total population of the three comparison groups was two, and the two clusters of psoriasis and atopic dermatitis were differentiated by gene expression. Our study suggests that clinical overlap phenotype between psoriasis and atopic dermatitis has dominant molecular features of psoriasis, and genomic biomarkers can differentiate psoriasis and atopic dermatitis at molecular levels in patients with a spectrum of psoriasis and atopic dermatitis.
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