Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues using PCT-SWATH.

PURPOSE: To rapidly identify protein abundance changes in biopsy-level fresh-frozen hepatocellular carcinoma (HCC).

EXPERIMENTAL DESIGN: We applied the pressure-cycling technology (PCT) and optimized sequential window acquisition of all theoretical mass spectra (SWATH-MS) workflow to analyze 38 biopsy-level tissue samples from 19 HCC patients. Each proteome was analyzed with 45 min liquid chromatography (LC) gradient. MCM7 was validated using immunohistochemistry (IHC).

RESULTS: We quantified 11,787 proteotypic peptides from 2,579 SwissProt proteins with high confidence. The coefficient of variation (CV) of peptide yield using PCT was 32.9%, and the R2 of peptide quantification was 0.9729. 541 proteins showed significant abundance change between the tumor area and its adjacent benign area. From 24 upregulated pathways and 13 suppressed ones, we observed enhanced biomolecule synthesis and suppressed small molecular metabolism in liver tumor tissues. We further analyzed protein changes based on α-fetoprotein expression and HBV infection. Our data altogether highlighted 16 promising tumor marker candidates. The up-regulation of minichromosome maintenance complex component 7 (MCM7) was further observed in multiple HCC tumor tissues by IHC.

CONCLUSIONS AND CLINICAL RELEVANCE: We demonstrated the practicality of rapid proteomic analysis of biopsy-level fresh-frozen HCC tissue samples with PCT-SWATH and identified promising tumor marker candidates including MCM7. This article is protected by copyright. All rights reserved.