Introduction

The term proteome comes from the study of gene-product mapping performed by the Ian Humphery-Smith and his group (1). They defined proteome as the total protein complement of a genome. Proteomics thus refers to the analysis of the total protein complement of a genome. Proteomics was the first of several succeeding developments of various studies such as transcriptomics, glycomics, and so on. The combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) is an effective method of high-throughput proteomics. The technique of 2-DE is able to differentiate proteins according to both their charges in isoelectoric focusing (IEF) gels and their size in sodium dodecyl sulfate (SDS) gels (2). The 2-DE technique has unique advantages for examining the expressions of hundreds of proteins simultaneously and also examining post-translational modifications of the protein spots. There are many reports of proteomics of diseases including cancer obtained by means of 2-DE (3,4,5). Recently, MS has become the first choice for determining sequences of proteins instead of the Edman method. By means of MS we can determine the masses of peptides with much accuracy, and from the huge database we can identify the protein (peptide mass fingerprinting) (6).

Many proteomic studies have identified diverse proteins that may be involved in the pathogenic mechanism of disease and which may be disease markers. Most of the applications use expression proteomics to determine expression profiles of proteins in cells and tissues in normal or disease states. In the present study, we analyzed protein expression in cancer tissue samples and corresponding non-cancerous tissue samples to find proteins that might be involved in carcinogenesis or pathogenesis.

Hepatocellular carcinoma (HCC) is the fifth most common and the third most deadly cancer. One million patients with HCC die each year. One of the major causes of HCC is infection with the hepatitis C virus (HCV), and the pathogenesis of HCV-related HCC in its incipient stage from the infection to the onset of cancer is being researched.

Esophageal cancer is the sixth leading cause of cancer death in Japan with a very high mortality rate. Many patients die within 1 year after diagnosis, and the 5-year survival rate is less than 10%. Pancreatic cancer is a cancer with a poor prognosis, having the lowest 5-year survival rate (7). To find tumor biomarkers or therapeutic drugs, many investigators are performing proteomic studies of cancer tissues and cancer cell lines, and the data are being accumulated (8,9). In this chapter, we will introduce the proteomics for HCC, pancreatic cancer, and esophageal cancer tissues performed by us, and also show the result of proteomic analysis of auto-antibodies in patients.

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