Spatial Multi-Omics Dissection of Astragaloside IV in Diabetic Kidney Zonation: A Food-Derived Bioactive Regulator of Metabolic and Proteomic Landscapes

• Spatial metabolome-proteome atlas of diabetic kidney zonation using MALDI-MSI, revealing region-specific metabolic dysregulation. • ASIV restores metabolic homeostasis in cortex (valine biosynthesis) and outer medulla (cysteine metabolism) via food-derived bioactivity. • Identified VNN1/ADH5/GMDS as urinary biomarkers (AUC>0.95) for diabetic nephropathy diagnosis, correlating with clinical indices. • ASIV reduces podocyte ROS/apoptosis via ADH5-mediated biological oxidation, validating a renoprotective food-bioactive mechanism. • WGCNA uncovered green module proteins (332) linked to cortex/inner medulla, regulating ubiquinone biosynthesis and renin-angiotensin signaling. Diabetic nephropathy (DN) is a major complication of diabetes, yet its metabolic and proteomic spatial dynamics remain poorly understood. Here, we integrate spatial metabolomics and proteomics to construct a high-resolution molecular atlas of diabetic mouse kidneys, revealing region-specific metabolic dysregulation and the therapeutic effects of Astragaloside IV (ASIV). Using MALDI mass spectrometry imaging (MALDI-MSI), we mapped the spatial distribution of metabolites across cortical (Cor), outer medullary (OM), and inner medullary (IM) regions, identifying 12 metabolites linked to DN progression. These metabolites were enriched in pathways such as linoleic acid metabolism, oxidative phosphorylation, and aminoacyl-tRNA biosynthesis. ASIV treatment restored metabolic homeostasis, particularly in Cor (valine biosynthesis) and OM (cysteine metabolism) regions. Spatial proteomics uncovered 95 ASIV-regulated proteins, including transporters (Cor), vitamin-binding proteins (OM), and oxidoreductases (IM), with pathway analysis highlighting arginine biosynthesis (Cor) and glutathione metabolism (OM). Weighted gene co-expression network analysis (WGCNA) further identified a green module (332 proteins) correlated with Cor/IM regions, implicating ubiquinone biosynthesis and renin-angiotensin signaling. In human DN patients, urinary proteomics revealed VNN1, ADH5 and GMDS as diagnostic biomarkers (AUC>0.95), correlating with renal dysfunction. Cellular assays confirmed ASIV’s role in reducing ROS and apoptosis in podocytes via ADH5-mediated biological oxidation. Our study provides the spatial multi-omics atlas of DN, linking anatomic zonation to metabolic dysfunction and ASIV’s renoprotective mechanisms. These findings advance precision medicine for DN by identifying region-specific therapeutic targets and non-invasive biomarkers.