Omics datasets of Deep metabolic dysfunction profiling and drug-host-microbe interactions in the Wilson's Disease gut-liver axis

The data correspond to a observational case–control study that investigated metabolic and lipidomic alterations in patients with Wilson’s disease (WD) compared with age- and sex-matched healthy controls. Participants with genetically confirmed WD (Leipzig score ≥4) receiving disease-specific treatment were included, while individuals with liver transplantation, other chronic liver diseases, relevant comorbidities, recent antibiotic or probiotic use, pregnancy, diabetes, or significant alcohol intake were excluded. Multi-omics analyses were performed in a discovery cohort of approximately 24–25 patients and validated in an independent subgroup, alongside 25 healthy controls whose biological samples and lifestyle data were collected under standardized conditions. Plasma metabolomic profiling was conducted using proton nuclear magnetic resonance (1H-NMR) spectroscopy to identify and quantify metabolites after standardized sample preparation, spectral acquisition, and normalization procedures. Complementary lipidomic profiling was performed using liquid chromatography–mass spectrometry (LC–MS), incorporating rigorous quality control, randomized sample analysis, internal standards, and statistical normalization to ensure analytical reliability. Together, these methodologies enabled comprehensive characterization of systemic metabolic and lipid alterations associated with Wilson’s disease.