Prediction of Biomarkers for Hepatocellular Carcinoma Based on Proteomics and Phosphoproteomics

Purpose: It is well recognized that the proteomic plays a critical role in hepatocellular carcinoma (HCC) progression. However, the mechanisms of these proteins, particularly those regulated by phosphorylation, remain incompletely understood. This study aims to systematically characterize stage-specific molecular features of HCC to elucidate the key proteins and post-translational modification (PTM) networks that drive malignant transformation, and to identify candidate core biomarkers and therapeutic targets. Patients and Methods: Relative quantitative proteomics and TMT-labeled quantitative phosphoproteomics were used to identify hepatocellular carcinoma tissue (HCT), adjacent noncancerous tissue (ANT), and liver cirrhosis tissue (LCT). Functional enrichment analysis was performed with the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO); upstream kinases were predicted using PhosphoSitePlus (PSP), and protein-protein interaction (PPI) data were downloaded from STRING for network scoring and downstream analyses. Results: Integrated profiling revealed coordinated alterations in protein abundance and phosphorylation in HCT that were absent between ANT and LCT, indicating non-linear, multi-pathway convergence during tumorigenesis. A multi-tier scoring scheme prioritized 12 overlapping core driver proteins, including fructose-bisphosphate aldolase B (ALDOB), fumarylacetoacetase (FAH), argininosuccinate synthase (ASS1), cytochrome P450 2C8 (CYP2C8), and cytochrome P450 4A11 (CYP4A11). These proteins were significantly enriched in lipid, amino-acid, and carbohydrate metabolic pathways. Notably, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) showed unchanged total protein abundance but a marked reduction in phosphorylation in HCT vs. LCT, indicating stage-specific regulation dominated by post-translational modification. Kinase prediction further suggested potential cross-pathway reprogramming of phosphorylation signaling. Conclusion: The cytochrome P450 enzymes CYP4A11 and CYP2C8 (lipid metabolism), the amino-acid metabolism enzymes ASS1 and FAH, and the carbohydrate metabolism enzymes ALDOB and GAPDH were identified as key regulatory proteins in HCC progression. Aberrant phosphorylation of ALDOB and phosphorylation-dependent regulation of GAPDH, together with cross-pathway signaling rewiring, provide novel mechanistic insights into HCC pathogenesis.