Structural proteomics reveals a coagulation–complement accessibility signature of macrovascular invasion in hepatocellular carcinoma

Macrovascular invasion (MVI) and extrahepatic spread (EHS) define the most aggressive, treatment-refractory hepatocellular carcinoma (HCC), yet blood-based markers that report the underlying protein-network biology are lacking. Conventional proteomics measures protein abundance but not the conformational and protein–protein-interaction (PPI) states that govern function. We applied covalent proteome painting (CPP)—a dimethylation-based accessibility assay that reads out binding-site openness—to matched tumor and serum, reasoning that intravascular tumor dissemination remodels plasma protein complexes in a manner detectable as changes in accessibility.

Eight treatment-native HCC patients were profiled by CPP using matched FFPE tumor and top-14– depleted serum on a Q Exactive Orbitrap HF. The 85 tumor–serum common proteins defined an 81-protein targeted panel, validated by multiple-reaction-monitoring (MRM) mass spectrometry with heavy stable-isotope-standard peptides (296 peptides; 3,717 light/heavy transition pairs) in 22 FFPE tumors and 22 matched sera. Accessibility was the light/heavy ratio (high, open; low, closed). We assessed differential accessibility, serum–tissue translatability, pathway enrichment, and biomarker/survival performance.

Aggressive disease showed broadly decreased protein accessibility. MVI-associated changes were directionally concordant between tumor and serum (Spearman ρ=0.21; 59% concordant), driven by coagulation and complement proteins (FGG, CTSD, LBP, C4BPA); the EHS axis did not translate. Decreased-accessibility proteins were enriched for complement–coagulation cascades and IGF/IGFBP transport. A six-protein serum accessibility signature discriminated MVI (leave-one-out cross-validated AUC 0.80; best single markers ceruloplasmin 0.83 and haemoglobin-α 0.77), and MVI status trended with shorter overall survival (log-rank p=0.06).

Accessibility-based serum proteomics captures MVI-associated protein-complex remodeling that abundance assays miss, nominating a coagulation/complement-anchored serum signature for vascular-invasive HCC that warrants prospective validation.