Protein expression profiles of chemo-resistant mixed phenotype liver tumors using laser microdissection and LC–MS/MS proteomics

Hepatocellular carcinoma (HCC) treated with trans-arterial chemoembolization (TACE) can later show areas of hepatocellular or cholangiocarcinoma (CC) differentiation. Biomarkers are required to define details in phenotype/pathogenesis of these HCC/CC regions, and similarities to their normal and classic counterparts. Proteins from laser microdissected FFPE tissue were in-gel digested and peptides analyzed by nano-HPLC–MS/MS. We identified 95 proteins with significant differential expression between HCC vs. CC regions. We also found significant differences in other tissue type comparisons. Some protein biomarkers are being reported here for the first time in the context of liver carcinogenesis and may be clinically useful.