Prediction of Multidimensional Post-Translational Modification Profiles in Idiopathic Pulmonary Fibrosis Based on Substrate Availability via Non-Targeted Metabolomics

Background Idiopathic pulmonary fibrosis (IPF) is a fatal, progressive interstitial lung disease characterized by abnormal fibroblast activation and excessive extracellular matrix deposition. Traditional epigenetic and omics studies are costly and technically complex; therefore, the ability to retrospectively predict and deduce complex post-translational modification (PTM) landscapes based on the abundance of small-molecule substrates has become a frontier in epimetabolomics. Methods In this study, high-resolution non-targeted metabolomics (LC-MS/MS) analysis was performed on lung tissue samples from 9 IPF patients and 3 healthy controls (HC). Global metabolomic profiles were evaluated using multivariate statistical analysis (PCA and OPLS-DA), and differentially expressed metabolites were screened based on VIP > 1 and P < 0.05. Subsequently, pathway mapping was performed using the KEGG and HMDB databases, and a “substrate-multi-modification” prediction model was constructed, covering lactylation, methylation, acetylation, glycosylation, succinylation, and phosphorylation modifications. Results A total of 2,325 metabolites were detected in lung tissue. Multivariate analysis indicated significant separation of metabolic profiles between the IPF group and the HC group (OPLS-DA, Q²=0.523). The 345 significantly differentially expressed metabolites (266 upregulated, 79 downregulated) exhibited a strong enrichment of modified substrates. Lactate (FC = 13.43) and lactate phosphate (FC = 11.47), products of glycolysis, were dramatically upregulated, predicting high levels of lysine lactylation (Kla) in the tissue; Arginine (FC = 19.94) and trimethyllysine (FC = 5.21) surged, predicting active arginine/lysine methylation (Kme/Rme); Increases in N-acetylmannosamine (FC = 6.08) and N-acetylglucosamine 1-phosphate (FC = 4.67) predicted a remodeling of O-GlcNAc glycosylation and acetylation (Kac); Enrichments of 2,2-dimethylsuccinic acid (FC = 5.31) and fructose-6-phosphate (FC = 15.64) corresponded to substrate overload for succinylation and multi-site phosphorylation (Pho), respectively. Conclusion The reversal of the characteristic small-molecule expression profile in IPF lung tissue essentially constitutes a “building block library” for downstream multidimensional protein post-translational modifications (PTMs). Predicting the PTM landscape by reverse engineering metabolite abundances not only significantly reduces the cost of multi-omics exploration but also provides a novel molecular window for deciphering the multi-phenotypic regulation of fibrosis.