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

Single-cell RNA sequencing analysis of AD skin biopsies revealed increased keratinocyte heterogeneity and enhanced immune cell communication compared to healthy controls.

• Analysis was performed on skin biopsies from five AD patients and four healthy controls.
• Both keratinocyte heterogeneity and intercellular communication network activity were elevated in AD samples.
• Integration of single-cell RNA sequencing with computational pharmacology provided a cellular and molecular basis for understanding the chronicity and recurrence characteristics of AD.

Intersection analysis between gut microbial metabolite-associated genes and skin pathology-related genes identified seven key bridging genes.

• The seven bridging genes identified were AKR1C2, GALE, GGH, NR4A1, PLA2G4B, and TYMS (six genes listed; abstract states seven).
• Functional annotation indicated these genes are primarily involved in vitamin precursor metabolism.
• The Eubacterium eligens group was identified as the specific gut microbiota influencing AD pathogenesis through these bridging genes.

The Eubacterium eligens group was found to influence AD pathogenesis mainly through vitamin precursor-mediated pathways that regulate systemic immune responses.

• A causal relationship between specific gut microbiota and AD risk was established at the genetic level.
• Functional annotation of the bridging genes indicated primary involvement in vitamin precursor metabolism.
• This mechanism provides genetic-level evidence supporting the gut-skin axis theory in AD.

Pseudotime trajectory analysis demonstrated dynamic temporal gene expression patterns during AD disease progression.

• Pseudotime trajectory inference was applied to single-cell RNA sequencing data.
• The analysis revealed dynamic changes in gene expression as disease progresses.
• This approach contributed to understanding the temporal aspects of AD pathogenesis.

Molecular docking revealed unexpectedly high-affinity binding between methotrexate and GALE that exceeded its binding affinity for the classical target TYMS.

• Methotrexate binding energy with GALE was -10.4 kcal/mol.
• Methotrexate binding energy with its classical target TYMS was -7.5 kcal/mol.
• The binding affinity of methotrexate for GALE was significantly higher than for TYMS, suggesting GALE is an important but previously unrecognized target of methotrexate in AD treatment.
• Molecular dynamics simulations confirmed the stable binding conformation of the protein-ligand complexes.

GALE was identified as a novel therapeutic target for atopic dermatitis.

• GALE was among the seven key bridging genes identified at the intersection of gut microbial metabolite-associated genes and skin pathology-related genes.
• Reverse drug prediction was used as part of the analytical pipeline to identify therapeutic relevance.
• Molecular docking and molecular dynamics simulations confirmed stable and high-affinity binding of methotrexate to GALE.
• The findings suggest GALE may represent an important but previously unrecognized mechanism of methotrexate action in AD.

The study established causal relationships between gut microbiota and AD risk at the genetic level.

• Multiple analytical approaches were integrated including single-cell RNA sequencing, intercellular communication network analysis, pseudotime trajectory inference, reverse drug prediction, molecular docking, and molecular dynamics simulations.
• The causal relationship was described as providing 'strong genetic evidence' for the gut-skin axis theory.
• Specific identification of the Eubacterium eligens group as causally linked to AD risk was achieved.