Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray

Moon Kim Tae, Jin Jeong Ha, Young Seo Min, Chul Kim Sang, Gabee Cho, Hee Park Chan, Soo Kim Tae, Hyun Park Kyu, Hyuncheol Chung, SunYoung Rha

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)79-86
Number of pages8
JournalClinical Cancer Research
Volume11
Issue number1
Publication statusPublished - 2005 Jan 1

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Gastrointestinal Neoplasms
Oligonucleotide Array Sequence Analysis
Cell Line
Genes
Microarray Analysis
Stomach Neoplasms
Neoplasms
RNA
Gene Expression
Gene Expression Profiling
Transcriptome
Reverse Transcription
Real-Time Polymerase Chain Reaction
Research Design
Genome
Databases
Lymphocytes
Phenotype
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Oncology
  • Cancer Research

Cite this

Tae, M. K., Ha, J. J., Min, Y. S., Sang, C. K., Cho, G., Chan, H. P., ... Rha, S. (2005). Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray. Clinical Cancer Research, 11(1), 79-86.
Tae, Moon Kim ; Ha, Jin Jeong ; Min, Young Seo ; Sang, Chul Kim ; Cho, Gabee ; Chan, Hee Park ; Tae, Soo Kim ; Kyu, Hyun Park ; Chung, Hyuncheol ; Rha, SunYoung. / Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray. In: Clinical Cancer Research. 2005 ; Vol. 11, No. 1. pp. 79-86.
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Tae, MK, Ha, JJ, Min, YS, Sang, CK, Cho, G, Chan, HP, Tae, SK, Kyu, HP, Chung, H & Rha, S 2005, 'Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray', Clinical Cancer Research, vol. 11, no. 1, pp. 79-86.

Determination of genes related to gastrointestinal tract origin cancer cells using a cDNA microarray. / Tae, Moon Kim; Ha, Jin Jeong; Min, Young Seo; Sang, Chul Kim; Cho, Gabee; Chan, Hee Park; Tae, Soo Kim; Kyu, Hyun Park; Chung, Hyuncheol; Rha, SunYoung.

In: Clinical Cancer Research, Vol. 11, No. 1, 01.01.2005, p. 79-86.

Research output: Contribution to journalArticle

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AU - Tae, Moon Kim

AU - Ha, Jin Jeong

AU - Min, Young Seo

AU - Sang, Chul Kim

AU - Cho, Gabee

AU - Chan, Hee Park

AU - Tae, Soo Kim

AU - Kyu, Hyun Park

AU - Chung, Hyuncheol

AU - Rha, SunYoung

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N2 - 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.

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