Gene expression based molecular test as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue, microbiopsies and tape strips
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ABSTRACT:
PROVIDER: PRJNA928395 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23244900_1.fastq.gz | Fastqsanger.gz | |||
| SRR23244900_2.fastq.gz | Fastqsanger.gz | |||
| SRR23245000_1.fastq.gz | Fastqsanger.gz | |||
| SRR23245000_2.fastq.gz | Fastqsanger.gz | |||
| SRR23244901_1.fastq.gz | Fastqsanger.gz |
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Project description:Development of a real-time PCR based molecular classifier to distinguish psoriasis from eczema in FFPE-fixed skin samples and evaluation of the use of minimally invasive microbiopsies and tape strips for molecular diagnosis.
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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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