Identification of novel candidate genes and predicted miRNAs in atopic dermatitis patients by bioinformatic methods

Abstract

Atopic dermatitis (AD) is a common, chronic inflammatory dermatosis with relapsing eruptions. Our study used bioinformatics to find novel candidate differentially expressed genes (DEGs) and predicted miRNAs between AD patients and healthy controls. The Mesh term “atopic dermatitis” was retrieved to obtain DEGs in GEO datasets. DEGs between AD patients and healthy controls were analyzed using GEO2R. Overlapping DEGs between different datasets were obtained with use of Draw Venn software. GO and KEGG enrichment analyses were conducted by the use of DAVID. STRING and miRWalk were used to individually analyze PPI networks, interactions of candidate genes and predicted miRNAs. A total of 571 skin samples, as retrieved from 9 databases were assessed. There were 225 overlapping DEGs between lesioned skin samples of AD patients and that of healthy controls. Nineteen nodes and 160 edges were found in the largest PPI cluster, consisting of 17 up-regulated and 2 down-regulated nodes. Two KEGG pathways were identified, including the cell cycle (CCNB1, CHEK1, BUB1B, MCM5) and p53 (CCNB1, CHEK1, GTSE1) pathways. There were 56 nodes and 100 edges obtained in the miRNA-target gene network, with has-miR-17-5p targeted to 4 genes and has-miR-106b-5p targeted to 3 genes. While these findings will require further verification as achieved with experiments involving in vivo and in vitro modles, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Screening differentially expressed genes and the pathogenesis in atopic dermatitis using bioinformatics

“…inflammatory pathways, and keratinization pathways (13)(14)(15). These results provide new directions and strategies for the treatment and prevention of AD and help to improve the quality of life and health of AD patients.…”

Reduced Filaggrin expression induces dysregulated intracellular signalling in atopic eczema

“…Profilaggrin is a predicted target for CAMK2 using phosphorylation-site prediction software (Sandilands et al, 2009) but this has not been explored mechanistically. Chen et al identified CAMK2D as a differentially expressed gene when comparing lesional and non-lesional AE skin to healthy controls using a pooled analysis of microarray datasets (L. H. Chen et al, 2022). However, CAMK2D is poorly enriched in the skin, so further work is necessary to establish if this protein has a role in barrier function or AE.…”