Yiqiang Xie, Dandan Xie, Sifan Guo, Zhibo Wang, Ying Cai, Xian Wang, Qiang Yang, Chunsheng Lin, Hong Yao, Qiqi Zhao, Yu Guan, Shi Qiu, Songqi Tang, Aihua Zhang
• Multi-omics links arginine/proline metabolism dysregulation to diabetic nephropathy (DN) across species. • Identifies ST13 lysine-14 acetylation as a key regulator of amino acid metabolism in DN pathogenesis. • Astragaloside IV (ASIV) protects against DN by inhibiting ST13(K14) acetylation, normalizing metabolic distribution. • Spatial MALDI-MSI reveals kidney cortex-specific spermidine/5′-methylthioadenosine accumulation in DN, regulated by ASIV. • Site-specific ST13 acetylation modulating amino acid metabolism offers a novel therapeutic avenue for DN. Diabetic nephropathy (DN) is one of serious complications of diabetes and severely weakens renal function. There is an urgent need in search for potential intervention targets, to improve our understanding of the pathological and therapeutic mechanisms of this disease. Understanding the molecular mechanisms of amino acid amino acid (AA) metabolism dysfunction in DN will help identify new therapeutic targets. We employed the targeted metabolomics, acetylation modification proteomics and spatial profiling to simultaneously analyze the metabolic modification-phenotype axis on the clinical patients, cells and DN mice. Multi-omics profiling in DN identified arginine/proline metabolism as the most perturbed pathway, with spermidine and 5’-methylthioadenosine exhibiting strong correlations to protein ST13 and clinical biomarkers. Significantly, astragaloside IV (ASIV) affected the metabolic and protein signatures in MPC-5 cells, especially identified spermidine and 5′-methylthioadenosine were ranked at top alteration and mainly involved in arginine biosynthesis and biosynthesis of amino acids. We systematically profiled 31 acetylated proteins were mainly associated with peptidyl-amino acid modification in kidney tissue from transgenic db/db mice. Interestingly, ASIV can significantly reduce the acetylated level of St13 at lysine 14 acetylation. Mass spectrometry imaging analysis also revealed kidney-spatial specific spermidine and 5′-methylthioadenosine were distributed in cortex, outer medulla and inter medulla region, respectively. Mechanistically, ASIV inhibited St13(K14) modification mediated spatial metabolism via regulating expression of AA. Our findings provided the protection mechanism of ASIV by inhibiting St13 acetylation at lysine 14 for regulating AA metabolism dysfunction, and highlighted site-specific acetylation modulating AA metabolism as a promising therapeutic avenue for DN disease.