Determination of Genes Related to Gastrointestinal Tract Origin Cancer Cells Using a cDNA Microarray

• Published in: Clinical cancer research 2005-01, Vol.11 (1), p.79-86
• Main Authors: Kim, Tae Moon, Jeong, Ha Jin, Seo, Min Young, Kim, Sang Chul, Cho, Gabee, Park, Chan Hee, Kim, Tae Soo, Park, Kyu Hyun, Chung, Hyun Cheol, Rha, Sun Young
• Format: Article
• Language: English
• Subjects: Antineoplastic agents; Biological and medical sciences; cancer cell line; cDNA microarray; Cell Line, Tumor; Cluster Analysis; Computational Biology; DNA Primers - chemistry; DNA, Complementary - metabolism; Fluorescent Dyes - pharmacology; Gastroenterology. Liver. Pancreas. Abdomen; Gastrointestinal Neoplasms - metabolism; gastrointestinal tract; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic; hematogenous metastasis; Humans; Medical sciences; Models, Biological; Multigene Family; Neoplasm Metastasis; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis - methods; Pharmacology. Drug treatments; Phenotype; Reverse Transcriptase Polymerase Chain Reaction; RNA - chemistry; RNA - metabolism; SAM; Stomach. Duodenum. Small intestine. Colon. Rectum. Anus; Tumors; Up-Regulation
• ISSN: 1078-0432; 1557-3265
• DOI: 10.1158/1078-0432.79.11.1

Purpose: We evaluated the genome-wide gene expression profiles of various cancer cell lines to identify the gastrointestinal tract cancer cell–related genes. Experimental Design: Gene expression profilings of 27 cancer cell lines and 9 tissues using 7.5K human cDNA microarrays in indirect design with Yonsei reference RNA composed of 11 cancer cell line RNAs were done. The significant genes were selected using significant analysis of microarray in various sets of data. The selected genes were validated using real-time PCR analysis. Results: After intensity-dependent, within-print-tip normalization by loess method, we observed that expression patterns of cell lines and tissues were substantially different, divided in two discrete clusters. Next, we selected 115 genes that discriminate gastrointestinal cancer cell lines from others using significant analysis of microarray. Among the expression profiles of five gastric cancer cell lines, 66 genes were identified as differentially expressed genes related to metastatic phenotype. YCC-16, which was established from the peripheral blood of one advanced gastric cancer patient, produced a unique gene expression pattern resembling the profiles of lymphoid cell lines. Quantitative real-time reverse transcription-PCR results of selected genes, including PXN , KRT8 , and ITGB5 , were correlated to microarray data and successfully discriminate the gastrointestinal tract cancer cell lines from hematologic malignant cell lines. Conclusions: A gene expression database could serve as a useful source for the further investigation of cancer biology using the cell lines.