Proteomics of Hepatitis C Virus and Hepatocellular Carcinoma

An extensive study by Wirth et al. [82] analyzed normal liver tissue and hepatoma-derived cell lines by 2D gel electrophoresis and N-terminal sequencing and identified a number of proteins that were differentially expressed between normal tissue and hepatoma cell lines. Similar studies have been performed by others as well [83,84]. However, these studies have used cell lines that have been in culture that may not accurately reflect all the changes seen in HCC. Comparison of liver tumor tissue with normal tissue would be ideal however, tissue heterogeneity is an issue and could confound the results [85]. Until only very recently [86,87], an infectious cell culture model for HCV has not been available. This new model system will allow for the identification of cellular proteins that are induced following HCV infection and further the development of a treatment for HCV. 

Two studies have used LC/MS/MS to identify differential protein expression in HIV- or HCV-infected cells. In the first study, traditional HPLC (ion exchange and reverse-phase columns) coupled to an ultrasensitive ion trap MS was employed to 

Some of the advantages include automation in sample application, ability to switch columns, and sensitivity, as this method is able to identify proteins at very low levels [107]. In addition, this method has been extensively used for the determination of drugs and hormone levels in human serum [108-111], making it a promising tool for the detection of disease prognosis markers. 

SELDI-TOF is a proteomic technology that aims at the quantitative analysis of protein mixtures. This technique relies on the use of trapping surfaces that allow differential capture of proteins based on intrinsic properties of the proteins themselves to identify proteins from crude samples without the need for an initial separation step. A small amount of sample can be directly applied to a biochip coated with specific chemical matrices (hydrophobic, cationic, or anionic) or specific biochemical materials, including DNA fragments or purified proteins. Bound proteins can then be analyzed by MS to obtain either the protein fingerprints or the amino acid sequence when interfaced with a tandem MS. 

In another study that evaluated the protein fingerprints of HIV-1-infected MDM, cell lysates were directly applied on two types of protein chips weak cation exchange and reverse-phase hydrophobic interaction. After washing to remove the unbound proteins, bound proteins were ionized and their molecular mass/charge ratio was determined using TOP analysis. Analysis of the obtained profiles showed distinct patterns between uninfected and infected MDM [33]. 

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