Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray.
OBJECTIVE
We evaluated the genome-wide gene expression profiles of various cancer cell lines to identify the gastrointestinal tract cancer cell-related genes.


METHODS
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.
Kim
Tae Moon
TM
Cancer Metastasis Research Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea.
Jeong
Ha Jin
HJ
Seo
Min Young
MY
Kim
Sang Chul
SC
Cho
Gabee
G
Park
Chan Hee
CH
Kim
Tae Soo
TS
Park
Kyu Hyun
KH
Chung
Hyun Cheol
HC
Rha
Sun Young
SY
D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000494:pharmacology; D005770:Gastrointestinal Neoplasms / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008954:Models, Biological; D005810:Multigene Family; D009362:Neoplasm Metastasis; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
D017931:DNA Primers; D018076:DNA, Complementary; D005456:Fluorescent Dyes; D012313:RNA