Spatial phosphoproteomics reveals regional phosphorylation features in liver cirrhosis progression

Liver cirrhosis (LC) is the end stage of chronic liver disease and is characterized by pseudolobule formation and extensive fibrosis. Protein phosphorylation, a key posttranslational modification, regulates cellular functions and disease progression. However, the dynamic changes in phosphorylation across different regions of cirrhotic liver tissue remain largely unexplored, thereby limiting mechanistic insights into LC pathogenesis.

We employed spatial phosphoproteomics combined with bioinformatics to analyze phosphorylation patterns in three LC tissue regions: the normal hepatocyte region (NH), the pseudolobular hepatocyte region (PH), and the fibrotic-inflammatory portal region (PII). The tissue samples were processed via laser capture microdissection (LCM), followed by phosphopeptide enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differential expression analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction (PPI) network construction, and kinase-substrate prediction were conducted to characterize spatial phosphorylation dynamics.

KEGG analysis revealed significant enrichment of ribosome, actin cytoskeleton regulation, and focal adhesion pathways among the upregulated differentially expressed phosphoproteins (DEPPs) from the PH/NH and PII/PH comparisons, whereas spliceosome alterations were observed among upregulated DEPPs of PH/NH and downregulated DEPPs of PII/PH. This study has identified several candidate molecules awaiting further validation, including the phosphorylated proteins IQGAP1 and VIM, as well as the kinases ERK and GSK3α, which may be implicated in the progression of LC.