• Reproductive and Developmental Biology
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• 제37권1호
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• pp.1-8
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• 2013

In order to investigate genetic stability and gene expression profile after cloning procedure, two groups of cloned pigs were used for swine leukocyte antigen (SLA) gene nucleotide alteration and microarray analyses. Each group was consist of cloned pigs derived from same cell line (n=3 and 4, respectively). Six SLA loci were analyzed for cDNA sequences and protein translations. In total, 16 SLA alleles were identified and there were no evidence of SLA nucleotide alteration. All SLA sequences and protein translations were identical among the each pig in the same group. On the other hand, microarray assay was performed for profiling gene expression of the cloned pigs. In total, 43,603 genes were analyzed and 2,150~4,300 reliably hybridized spots on the each chip were selected for further analysis. Even though the cloned pigs in the same group had identical genetic background, 18.6~47.3% of analyzed genes were differentially expressed in between each cloned pigs. Furthermore, on gene clustering analysis, some cloned pigs showed abnormal physiological phenotypes such as inflammation, cancer or cardiomyopathy. We assumed that individual environmental adaption, sociality and rank in the pen might have induced these different phenotypes. In conclusion, the results of the present study indicate that SLA locus genes appear to be stable following SCNT. However, gene expressions and phenotypes between cloned pigs derived from the same cell line were not identical even under the same rearing conditions.

• Clinical and Experimental Reproductive Medicine
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• 제39권2호
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• pp.87-93
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• 2012

Objective: Lin28 has been known to control the proliferation and pluripotency of embryonic stem cells. The purpose of this study was to determine the downstream effectors of Lin28 in mouse embryonic stem cells (mESCs) by RNA interference and microarray analysis. Methods: The control siRNA and Lin28 siRNA (Dharmacon) were transfected into mESCs. Total RNA was prepared from each type of transfected mESC and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis to confirm the downregulation of Lin28. The RNAs were labeled and hybridized with an Affymetrix Gene-Chip Mouse Genome 430 2.0 array. The data analysis was accomplished by GenPlex 3.0 software. The expression levels of selected genes were confirmed by quantitative real-time RT-PCR. Results: According to the statistical analysis of the cDNA microarray, a total of 500 genes were altered in Lin28-downregulated mESCs (up-regulated, 384; down-regulated, 116). After differentially expressed gene filtering, 31 genes were selected as candidate genes regulated by Lin28 downregulation. Among them, neuropeptide Y5 receptor and oocyte-specific homeobox 5 genes were significantly upregulated in Lin28-downregulated mESCs. We also showed that the families of neuropeptide Y receptor (Npyr) and oocyte-specific homeobox (Obox) genes were upregulated by downregulation of Lin28. Conclusion: Based on the results of this study, we suggest that Lin28 controls the characteristics of mESCs through the regulation of effectors such as the Npyr and Obox families.

• Journal of Plant Biotechnology
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• 제35권2호
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• pp.133-140
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• 2008

DNA와 histone 단백질의 변형은 식물 발달에 상당히 중요한 역할을 하는 것으로 알려져 있다. 식물 조직 배양 및 식물 발달 단계에서 methylation의 영향을 알아보고자 벼 종자로부터 캘러스 형성 및 식물체 재분화 단계에서 demethylation 물질인 5-azacytidine을 처리하여 유전자 발현 양상을 분석하였다. 식물체로의 재분화 능력이 있는 벼 배상체 캘러스는 5-azaC가 첨가된 H6A 배지에서는 형성되지 않았으며 갈색을 띠는 캘러스가 형성되었다. 또한 정상적인 캘러스를 5-azaC가 첨가된 MSRA 재분화 배지에서 배양했을 때도 대조구와는 달리 식물체 재분화는 이루어지지 않았다. 이러한 결과는 5-azaC가 정상적인 배상체 캘러스 및 shoot 분화에 부정적인 영향을 미친다는 것을 나타냈으며 따라서 DNA methylation이 식물 조직배양에서의 정상적인 세포 dedifferentiation과 differentiation에 필수 요인이라는 것을 알 수 있었다. 벼 캘러스 형성 및 재분화 과정 동안의 methylation 영향을 알아보고자 각 단계별로 5-azaC를 처리 후 $GeneFishig^{TM}$ DEG와 DNA chip을 사용하여 유전자 발현 양상을 분석하였다. Epigenetic regulation, 전자전달, 핵산대사, 스트레스 반응에 관여하는 일부 유전자들의 발현이 증가하거나 감소하는 것을 알 수 있었다. 발현 차이가 있는 일부 유전자를 클로닝하여 확인하였고 RT-PCR 및 northern 분석으로 각 단계에서의 발현 차이를 할인하였다.

• Journal of Animal Science and Technology
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• 제50권4호
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• pp.475-484
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• 2008

본 연구는 retinoic acid(RA)가 돼지지방전구세포의 분화와 유전자 발현에 미치는 영향을 구명하기 위해서 수행하였다. 지방전구세포는 갓난 돼지의 등지방에서 분리했으며 RA는 배양중인 세포에 4일 동안 처리하였다. 배양중인 세포에서 RNA를 추출한 후 14,688개의 유전자가 부착되어 있는 cDNA microarray와 혼성화 하여 유전자 발현 양상을 분석하였다. 지방전구세포의 분화는 GPDH의 활성도에 의해 측정했다. RA는 돼지지방전구세포의 분화를 78% 억제했다. Retinoic acid 처리에 의해 지질 대사에 관계된 유전자를 포함하여 특히 sphin- gomyelin phosphodiesterase, apolipoprotein R precursor, growth factor receptor-bound protein 14, retinoic receptor RXR gamma의 발현이 증가 되었다. 그리고 세포 성장에 중요 역할을 하는 vascular endothelial growth factor D precursor, growth hormone receptor precursor의 유전자의 발현이 감소되었다. 이러한 결과는, RA가 성장촉진인자 또는 성장호르몬 수용체의 조절을 통해서 돼지 지방전구세포의 분화를 억제함을 나타낸다.

• Mycobiology
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• 제38권2호
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• pp.144-148
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• 2010

$\beta$-Glucans have been known to exhibit antitumor activities by potentiating host immunity by an unknown mechanism. The C-type lectin dectin-1, a $\beta$-glucan receptor, is found on the macrophage and can recognize various $\beta$-glucans. Previously, we demonstrated the presence of $\beta$-glucan receptor, dectin-1, on the Raw 264.7 cells as well as on murine mucosal organs, such as the thymus, the lung, and the spleen. In order to investigate immunopotentiation of innate immunity by $\beta$-glucan, we stimulated a murine macrophage Raw 264.7 cell line with $\beta$-glucans from Pleurotus ostreatus, Saccharomyces cerevisiae, and Laminaria digitata. Then, we analyzed cytokines such as tumor necrosis factor (TNF)-$\alpha$ and interleukin (IL)-6 by reverse transcription-polymerase chain reaction (RT-PCR). In addition we analyzed gene expression patterns in $\beta$-glucan-treated Raw 264.7 cells by applying total mRNA to cDNA microarray to investigate the expression of 7,000 known genes. When stimulated with $\beta$-glucans, the macrophage cells increased TNF-$\alpha$ expression. When co-stimulation of the cells with $\beta$-glucan and lipopolysaccharide (LPS), a synergy effect was observed by increased TNF-$\alpha$ expression. In IL-6 expression, any of the $\beta$-glucans tested could not induce IL-6 expression by itself. However, when co-stimulation occurred with $\beta$-glucan and LPS, the cells showed strong synergistic effects by increased IL-6 expression. Chip analysis showed that $\beta$-glucan of P. ostreatus increased gene expressions of immunomodulating gene families such as kinases, lectin associated genes and TNF-related genes in the macrophage cell line. Induction of TNF receptor expression by FACS analysis was synergized only when co-stimulated with $\beta$-glucan and LPS, not with $\beta$-glucan alone. From these data, $\beta$-glucan increased expressions of immunomodulating genes and showed synergistic effect with LPS.

• 한방안이비인후피부과학회지
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• 제22권1호
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• pp.11-32
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• 2009

Objective : This study was designed to investigate anti-cancer and whitening activities (LC). So it was investigated the effects of LC on proliferation rates of melanoma genetic profile by LC. Methods : The genetic profile for the effect of LC on human derived melanoma cell, SK-MEL-2, was measured using microarray technique, and the functional analysis on these genes were conducted. Total 441 genes were up-regulated and 830 genes down-regulated in cells treated with LC. Genes induced or suppressed by LC were all mainly concerned with basic signalling pathways, which are involved in cell growth, differentiation and migration. Especially, many genes, which are related in apoptosis and cell cycle arrest were up-regulated by treatment with LC, and genes related in cell cycle were down-regulated. Result : The network of total protein interactions were identified by using cytoscape program, and some key molecules, such as BCL2L1, SIN3A, SMAD2 and c-myc that can be used for elucidation of therapeutical mechanism of medicine in the future. Conclusion : These results suggest possibility of LC as addition drug and whitening cosmetics. In addition, it was also suggested that related mechanisms are involved in BCL2L1, SIN3A, SMAD2 and c-myc related signalling pathways.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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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.

• Molecular & Cellular Toxicology
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• 제3권2호
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• pp.98-106
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• 2007

Genotoxic stress triggers a variety of biological responses including the transcriptional activation of genes regulating DNA repair, cell survival and cell death. In this study, we investigated to examine gene expression profiles and genotoxic response in TK6 cells treated with DNA damaging agents MNNG (N-methyl-N'-nitrosoguanidine) and hydrogen peroxide $(H_2O_2)$. We extracted total RNA in three independent experiments and hybridized cRNA probes with oligo DNA chip (Applied Biosystems Human Genome Survey Microarray). We analyzed raw signal data with R program and AVADIS software and identified a number of deregulated genes with more than 1.5 log-scale fold change and statistical significancy. We indentified 14 genes including G protein alpha 12 showing deregulation by MNNG. The deregulated genes by MNNG represent the biological pathway regarding MAP kinase signaling pathway. Hydrogen peroxide altered 188 genes including sulfiredoxins. These results show that MNNG and $H_2O_2$ have both uniquely regulated genes that provide the potential to serve as biomarkers of exposure to DNA damaging agents.

• 동의생리병리학회지
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• 제19권4호
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• pp.913-921
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• 2005

In this study, we investigated gene expression patterns induced by Ailanthus altissima extract and compared it with Gleevec, a well-known anti-leukemia drug, in K562 chromic leukemia cells. Ailanthus altissima extract(100 ug/ml) and Gleevec(50 ug/ml) were treated to cells for 1h, 2h, 4h, and 16h and total RNA was extracted. Gene expressions were evaluated using cDMA microarray, in which 24,000 genes were spotted. Hierarchical clustering analysis showed that expression of genes included in two clusters were increased or decreased time dependently by both Ailanthus altissima extract and Gleevec. Genes included in another cluster were induced by Ailanthus altissima extract but not by Gleevec. In biological process analysis, expression of genes involved in apoptosis, growth arrest and DNA-damage were increased, but genes stimulating cell cycle were decreased. This study provides comprehensive comparison of the patterns of gene expression changes induced by Ailanthus altissima extract and Gleevec in K-562 leukemia cells.

• Molecular & Cellular Toxicology
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• 제1권4호
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• pp.275-280
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• 2005

Carbon tetrachloride ($CCl_4$) is well known hepatotoxicant. Its overdose cause severe centrilobular hepatic necrosis in human and experimental animals. We administered $CCl_{4}$ at low (0.2 mL/kg p.o.) and high (2 mL/kg p.o.) doses to mice. Mice were sacrificed at 24 h after administration. We evaluated liver toxicity by serum AST and ALT level and by microscopic observation. Using cDNA chip, we conducted gene expression analysis in liver. Mean serum activities of the hepatocellular leakage enzymes, ALT and AST, were significantly increased compare to control, respectively, in the low and high dose groups. H&E evaluation of stained liver sections revealed $CCl_{4}-related$ histopathological findings in mice. Moderate centrilobular hepatocellular necrosis was present in all $CCl_{4}$ treated mice. We found that gene expression pattern was very similar between low and high dose group. However, some stress related genes were differently expressed. These results could be a molecular signature for the degree of liver injury. Our data suggest that the degree of severity could be figure out by gene expression profiling.