Integrative metabolomics and malonyl-proteomics reveal the crosstalk between metabolic reprogramming and lysine malonylation in liver fibrosis.

Lysine malonylation (Kmal), a recently identified post-translational modification (PTM) of proteins, has been linked to energy metabolism and implicated in various pathological disorders, including liver diseases. However, the specific roles of Kmal in hepatic fibrosis remain enigmatic. This study aims to investigate novel post-translational modifications and the underlying mechanisms involved in liver fibrosis. Utilizing untargeted metabolomics on carbon tetrachloride (CCl4)-induced mouse fibrotic liver tissues, we observed significant metabolic dysregulation during the liver fibrotic process, characterized by notably increased levels of malonyl coenzyme A (CoA). Additionally, the fibrotic liver tissues exhibited dramatically elevated Kmal levels and a high abundance of acetyl-CoA carboxylase 1 (ACC1), an enzyme essential for converting acetyl-CoA to malonyl-CoA, compared to normal liver tissues. Furthermore, 4D label-free malonylation quantitative proteomics was employed to characterize the malonyl proteome in fibrotic liver tissues. A total of 3,512 malonylated sites in proteins were identified, revealing significant enrichment in metabolism-related pathways, such as the urea cycle, TCA cycle, and fatty acid biosynthesis and oxidation. And both the protein expression status and Kmal level of ACSL4 was significantly upregulated in fibrotic liver tissues. Collectively, these results illuminate a potential regulatory mechanism of energy metabolism and underscore the significance of Kmal for future therapeutic development in liver fibrosis.