Pancreatic ductal carcinoma-specific genes identified by DNA microarray analysis with ductal cells

Abstract

Pancreatic ductal carcinoma (PDC) remains the most intractable disorder amonggastroenterological malignancies, with a 5-year survival rate of <5%. Given the low 5-year survival rate even of individuals with small, resectable tumors, the sensitivity of current technologies is not sufficient to allow detection of pancreatic carcinoma at curable early stages. A cure for this disorder will thus depend on development of an approach that is able to detect tumors at an early stage of carcinogenesis. DNA microarray analysis allows the simultaneous monitor[ng of the expression of thousands of genes and is therefore a potentially suitable approach to identify PDC-specific genes. The high throughput of this methodology also may be disadvantageous, however. Without careful selection of samples for analysis or data normalization procedures, DNA microarray experiments yield a large number of pseudopositive and pseudonegative results We therefore adopted the strategy of background-matched population (BAMP) screening, in which the sample characteristics are matched as closely as possible, with the exception of the feature of interest (in this case, transformation), before microarray analysis. To achieve this goal, we purified pancreatic carcinoma cells and normal ducta[ cells from pancreatic juice with the use of affinity chromatography based on the shared surface marker MUC1. Analysis of these background-matched samples with DNA microarrays representing 33000 human genes resulted in the identification of several carcinoma-specific genes, including those for AC133 and carcinoembryonic antigen-related cell adhesion molecule 7 (CEACAM7) Cancer-specific expression of these genes was confirmed by quantitative real-time polymerase chain reaction analysis. Microarray analysis with purified pancreatic ducta[ cells has thus provided a basis for the development of a sensitive method for the detection of PDC that relies on pancreatic juice, which is routinely obtained in the clinical setting