title: In-house cDNA microarray analysis of gene expression profiles involved in SCC cell lines.
abstract: To analyze gene expression in oral cancer, we produced a specialized in-house cDNA microarray. The cDNA library was constructed from surgical specimens of oral squamous cell carcinoma (SCC) using an oligo-capping method. cDNA clones (n=4,800) were randomly selected and their 5'-end nucleotide sequences were determined. Overlapping clones were excluded, and 1,423 independent clones were selected and used for microarray production. Compared to the public nucleotide sequence database, 61% of our cDNA clones were full-length. By correlating expression patterns across SCC cell lines, we identified 53 genes (7 up-regulated and 46 down-regulated) that are differentially expressed in SCC cell lines compared to normal mucosa. Semi-quantitative RT-PCR analysis confirmed these findings and validity of our cDNA microarray. Using specimens from SCC patients, we investigated the expression status of the IL-1ra gene, which showed the down-regulated gene by microarray analysis. Gene expression clearly fell in the SCC specimens relative to their references, which indicated that our in-house cDNA microarray system rapidly identified and characterized candidate biomarkers for clinical use.
authors.affiliation: Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
authors.forename: Tetsuhiro
authors.initials: T
authors.lastname: Moriya
authors.forename: Naohiko
authors.initials: N
authors.lastname: Seki
authors.forename: Ken
authors.initials: K
authors.lastname: Shimada
authors.forename: Masaki
authors.initials: M
authors.lastname: Kato
authors.forename: Takashi
authors.initials: T
authors.lastname: Yakushiji
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Nimura
authors.forename: Katsuhiro
authors.initials: K
authors.lastname: Uzawa
authors.forename: Masaki
authors.initials: M
authors.lastname: Takiguchi
authors.forename: Hideki
authors.initials: H
authors.lastname: Tanzawa
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism*; D045744:Cell Line, Tumor; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism; D019992:Databases as Topic; D015536:Down-Regulation; D015972:Gene Expression Regulation, Neoplastic; D015723:Gene Library; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D004247:DNA