• Title/Summary/Keyword: Functional genomics

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Identification of Novel Genes with Proapoptotic Activity

  • Kang Eun-Ju;Kim Jeong-Min;Kim Na-Young;Park Kyung-Mi;Park Seong-Min;Kim Nam-Soon;Yoo Hyang-Sook;Yeom Young-Il;Kim Soo-Jung
    • Genomics & Informatics
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    • v.4 no.2
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    • pp.77-79
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    • 2006

  • In order to identify novel proapoptotic genes, we screened approximately 1,000 hypothetical genes whose functions are completely unknown. After these genes were transiently expressed in HeLa cells, their nuclei images were captured using automated high-speed fluorescence microscope, through which the ratio of apoptotic nuclei was estimated. We selected genes that induce greater than 3-fold increase in apoptotic nuclei compared to that of the vector control. The candidate proapoptotic genes were sequenced and their effects on cell death were further confirmed by the additional assay, DNA fragmentation ELISA. Finally, we were able to identify 4 full-length hypo-thetical genes with proapoptotic activity.

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Identification of Novel Regulators of Apoptosis Using a High-Throughput Cell-based Screen

  • Park, Kyung Mi;Kang, Eunju;Jeon, Yeo-Jin;Kim, Nayoung;Kim, Nam-Soon;Yoo, Hyang-Sook;Yeom, Young Il;Kim, Soo Jung
    • Molecules and Cells
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    • v.23 no.2
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    • pp.170-174
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    • 2007

  • High-throughput subcellular imaging is a powerful tool for investigating the function of genes. In order to identify novel regulators of apoptosis we transiently transfected HeLa cells with 938 hypothetical genes of unknown function, and captured their nuclear images with an automated fluorescence microscope. We selected genes that induced greater than 3-fold increase in the percentage of apoptotic nuclei compared with vector-transfected cells. The full-length genes C10orf61, MGC 26717, and FLJ13855 were identified as candidate proapoptotic genes, and their apoptotic effects were confirmed by DNA fragmentation ELISAs and Western blotting for caspase-7 and PARP. We conclude that a subcellular image-based apoptotic screen is useful for identifying genes with proapoptotic activity.

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Novel target genes of hepatocellular carcinoma identified by chip-based functional genomic approaches

  • Kim Dong-Min;Min Sang-Hyun;Lee Dong-Chul;Park Mee-Hee;Lim Soo-Jin;Kim Mi-Na;Han Sang-Mi;Jang Ye-Jin;Yang Suk-Jin;Jung Hai-Yong;Byun Sang-Soon;Lee Jeong-Ju;Oh Jung-Hwa
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2006.02a
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    • pp.83-89
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    • 2006

  • Cellular functions are carried out by a concerted action of biochemical pathways whose components have genetic interactions. Abnormalities in the activity of the genes that constitute or modulate these pathways frequently have oncogenic implications. Therefore, identifying the upstream regulatory genes for major biochemical pathways and defining their roles in carcinogenesis can have important consequences in establishing an effective target-oriented antitumor strategy We have analyzed the gene expression profiles of human liver cancer samples using cDNA microarray chips enriched in liver and/or stomach-expressed cDNA elements, and identified groups of genes that can tell tumors from non-tumors or normal liver, or classify tumors according to clinical parameters such as tumor grade, age, and inflammation grade. We also set up a high-throughput cell-based assay system (cell chip) that can monitor the activity of major biochemical pathways through a reporter assay. Then, we applied the cell chip platform for the analysis of the HCC-associated genes discovered from transcriptome profiling, and found a number of cancer marker genes having a potential of modulating the activity of cancer-related biochemical pathways such as E2F, TCF, p53, Stat, Smad, AP-1, c-Myc, HIF and NF-kB. Some of these marker genes were previously blown to modulate these pathways, while most of the others not. Upon a fast-track phenotype analysis, a subset of the genes showed increased colony forming abilities in soft agar and altered cell morphology or adherence characteristics in the presence of purified matrix proteins. We are currently analyzing these selected marker genes in more detail for their effects on various biological Processes and for Possible clinical roles in liver cancer development.

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