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Profiling transcriptomic changes and signaling pathways in atopic dermatitis by integrative analyses on multiple databases

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Abstract

Atopic dermatitis (AD) is a condition driven by T cell-mediated immune response. Targeted therapy of AD is challenging due to its complex pathogenesis. In the current study, by analyzing multiple expression and network datasets, we aimed at: (1) identifying important transcriptomic signatures/profiles for AD to seek potential therapeutic targets and (2) discovering key regulators in the pathogenesis of AD. Our differentially expressed gene (DEG) analysis revealed multiple genes involved in immune response and dermal structural integrity. Functional enrichment analyses suggested that signaling pathways involved in epidermal barrier and inflammation and immunity are overrepresented in lesional AD. Protein–protein interaction (PPI) network and causal interactions analyses highlighted the roles of regulators of epidermal integrity and immune response in the pathogenesis of AD. Prominently, a negative regulator of the B-cell receptor-mediated immune response, PKCβ, has been suggested in the predicted pathogenesis model for AD, implying B cell-mediated immune response may play an equally important role as that of the T cell-mediated immune response in AD. A further search in a perturbagen database has identified small molecular drugs that may alter expression profiles of key regulators in the pathogenesis of AD. In this study, we propose a systemic multi-omics strategy incorporating multiple analyses on various datasets of transcriptomes, diseases, and pharmacology. Such integrative analyses will effectively advance our understanding on the pathogenesis and treatment of AD.

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Availability of data and material

All datasets are available in open public repositories, with information/links indicated in the "Materials and methods" section.

Code availability

Details of all software and codes used in the current study have been indicated in the "Materials and methods" section.

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  1. Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000, Zhejiang, China

    Yubin Xu, Saizhen Chen & Jinguang Chen

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  1. Yubin Xu
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  2. Saizhen Chen
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Correspondence to Jinguang Chen.

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Xu, Y., Chen, S. & Chen, J. Profiling transcriptomic changes and signaling pathways in atopic dermatitis by integrative analyses on multiple databases. Mol Genet Genomics 296, 341–353 (2021). https://doi.org/10.1007/s00438-020-01754-x

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