# Genome-wide identification of dysregulated alternative splicing and RNA-binding proteins involved in atopic dermatitis

## TL;DR

This study identifies dysregulated RNA-binding proteins and alternative splicing events in atopic dermatitis, suggesting they may play a key role in the disease's development.

## Contribution

The paper presents a genome-wide analysis linking dysregulated RBPs and RASEs to immune and inflammatory pathways in atopic dermatitis.

## Key findings

- 60 differentially expressed RBP genes were identified, mostly upregulated in lesional AD skin and linked to immune and apoptosis pathways.
- Alternative splicing events (alt3p and alt5p) were more prevalent in non-lesional and lesional AD skin compared to healthy skin.
- Four genes (IFI16, S100A9, PKM, ENO1) were upregulated in AD patient PBMCs, aligning with DE-RBP gene analysis.

## Abstract

Objectives: We explored the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of atopic dermatitis (AD).

Methods: We downloaded RNA-seq data (GSE121212) from 10 healthy control skin samples (healthy, Ctrl), 10 non-lesional skin samples with AD damage (non-lesional, NL), and 10 lesional skin samples with AD damage (lesional, LS). We performed the analysis of differentially expressed genes (DEGs), differentially expressed RBPs (DE-RBPs), alternative splicing (AS), functional enrichment, the co-expression of RBPs and RASEs, and quantitative polymerase chain reaction (qPCR).

Results: We identified 60 DE-RBP genes by intersecting 2141 RBP genes from existing reports with overall 2697 DEGs. Most of the DE-RBP genes were found to be upregulated in the AD LS group and related to immune and apoptosis pathways. We observed different ASEs and RASEs among the healthy, AD NL, and AD LS groups. In particular, alt3p and alt5p were the main ASEs and RASEs in AD NL and AD LS groups, compared to the healthy group. Furthermore, we constructed co-expression networks of DE-RBPs and RAS, with particular enrichment in biological pathways including cytoskeleton organization, inflammation, and immunity. Subsequently, we selected seven genes that are commonly present in these three pathways to assess their expression levels in the peripheral blood mononuclear cells (PBMCs) from both healthy individuals and AD patients. The results demonstrated the upregulation of four genes (IFI16, S100A9, PKM, and ENO1) in the PBMCs of AD patients, which is highly consistent with DE-RBP genes analysis. Finally, we selected four RAS genes regulated by RBPs that were related to immune pathways and examined their RASEs in PBMCs from both AD patients and healthy controls. The results revealed an increased percentage of RASEs in the DDX60 gene in AD, which is highly consistent with AS analysis.

Conclusion: Dysregulated RBPs and their associated RASEs may have a significant regulatory role in the development of AD and could be potential therapeutic targets in the future.