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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq.

Tu Hu^1,2, Tanja Todberg^3,4, Daniel Andersen⁵

¹Bioinformatics, Molecular Biomedicine, LEO Pharma A/S, 2750 Ballerup, Denmark.

International Journal of Molecular Sciences

|June 10, 2022

Summary

Tape stripping effectively assesses the atopic dermatitis (AD) transcriptome using BRB-seq, identifying 91 key genes. Deeper sequencing is recommended for reliable, population-wide screening of this inflammatory skin condition.

Keywords:

BRB-seq atopic dermatitis epidermis tape stripping transcriptome

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Area of Science:

Dermatology
Genomics
Molecular Biology

Background:

Atopic dermatitis (AD) is an inflammatory skin disorder with a compromised skin barrier.
Tape stripping is a non-invasive method for obtaining skin samples to study gene expression.
Transcriptomic profiling of AD using tape stripping requires optimized methods.

Purpose of the Study:

To evaluate the efficacy of BRB-seq for assessing the epidermal transcriptome in atopic dermatitis (AD) using tape-stripped skin samples.
To identify a gene expression signature characteristic of AD in the epidermis.
To compare transcriptomic data from tape-stripped skin with full-thickness biopsies.

Main Methods:

BRB-seq, a low-cost transcriptomic profiling technique, was applied to tape-stripped skin samples from 30 AD patients and 30 healthy controls.
Differential gene expression analysis was performed to identify an AD signature.
Correlation analysis was conducted between tape-stripped skin and matched full-thickness punch biopsies.

Main Results:

An AD signature of 91 differentially expressed genes related to skin barrier and inflammation was identified.
Gene expression in the stratum corneum and stratum granulosum from tape-stripped skin showed high correlation with punch biopsies.
Low and variable transcript counts due to RNA yield and degradation were observed, limiting profiling compared to punch biopsies.

Conclusions:

BRB-seq can profile the epidermal transcriptome in AD using tape-stripped skin, identifying a relevant gene signature.
Tape stripping provides transcriptomic data comparable to punch biopsies for the outermost skin layers.
Deep BRB-seq is necessary to overcome RNA yield variability and data inflation for population-wide screening in inflammatory skin diseases.