Integrative multi-omics analysis reveals gut-skin axis mechanisms and novel therapeutic target GALE in atopic dermatitis.

UNLABELLED: The gut-skin axis represents a critical but poorly understood pathway in atopic dermatitis (AD) pathogenesis. This study aimed to establish causal relationships between gut microbiota and AD risk while identifying key molecular bridges and therapeutic targets. We integrated multiple analytical approaches, including single-cell RNA sequencing analysis of skin biopsies from five AD patients and four healthy controls, intercellular communication network analysis, pseudotime trajectory inference, reverse drug prediction, molecular docking, and molecular dynamics simulations. Analysis revealed increased keratinocyte heterogeneity and enhanced immune cell communication in atopic dermatitis (AD) samples. Intersection analysis between gut microbial metabolite-associated genes and skin pathology-related genes identified seven key bridging genes (AKR1C2, GALE, GGH, NR4A1, PLA2G4B, TYMS). Functional annotation indicated that these genes are primarily involved in vitamin precursor metabolism, suggesting that the Eubacterium eligens group influences AD pathogenesis mainly through vitamin precursor-mediated pathways that regulate systemic immune responses. Pseudotime trajectory analysis demonstrated dynamic temporal gene expression patterns during disease progression. Molecular docking revealed an unexpectedly high-affinity binding between methotrexate and GALE (binding energy = -10.4 kcal/mol), which exceeded its binding affinity for the classical target TYMS (-7.5 kcal/mol). Molecular dynamics simulations further confirmed the stable binding conformation of the protein-ligand complexes. This study provides mechanistic insights into how the Eubacterium eligens group influences atopic dermatitis through vitamin precursor-mediated systemic immune modulation and identifies GALE as a novel therapeutic target. The findings provide mechanistic insights into the gut-skin axis and support developing precision medicine approaches integrating microbiome interventions with targeted pharmacotherapy for AD management.

IMPORTANCE

Genetic-level evidence of gut microbiota causality in atopic dermatitis: this study established a causal relationship between specific gut microbiota and the risk of atopic dermatitis at the genetic level, providing strong genetic evidence for the "gut-skin axis" theory. GALE is identified as a novel therapeutic target with redefined methotrexate mechanism: molecular docking study unexpectedly found that GALE binding affinity of MTX was significantly higher than that of its classical target TYMS, suggesting that GALE may be an important but previously unrecognized target of MTX in the treatment of AD. Multi-omics integration framework reveals increased keratinocyte heterogeneity: integrating single-cell RNA sequencing and computational pharmacology provided a cellular and molecular basis for understanding the characteristics of chronicity and recurrence of the disease.