• Toxicological Research
• /
• 제27권1호
• /
• pp.43-48
• /
• 2011

Even though exposure to benzene has been linked to a variety of cancers including leukemia, the detailed molecular mechanisms relevant to benzene-induced carcinogenesis remain to be clearly elucidated. In this study, we evaluated the effects of benzene on differential gene expression in a leukemia cell line. The K562 leukemia cell line used in this study was cultured for 3 h with 10 mM benzene and RNA was extracted. To analyze the gene expression profiles, a 41,000 human whole genome chip was employed for cDNA microarray analysis. We initially identified 6,562 genes whose expression was altered by benzene treatment. Among these, 3,395 genes were upregulated and 3,167 genes were downregulated by more than 2-fold, respectively. The results of functional classification showed that the identified genes were involved in biological pathways including transcription, cell proliferation, the cell cycle, and apoptosis. These gene expression profiles should provide us with further insights into the molecular mechanisms underlying benzene-induced carcinogenesis, including leukemia.

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

• 생명과학회지
• /
• 제19권8호
• /
• pp.1159-1163
• /
• 2009

ER stress에 관련된 유전자의 기능변화와 전사조절인자 분석하기 위해 ER stress를 유도한 간세포에서 expression microarray로 유전자 발현을 확보한 후 GSECA로 분석하였다. ER stress가 유도되면, ER에 주어지는 과도한 부하를 감소시키는 기능들이 증가하는 반면, ER stress가 더 증가함에 따라 ATP 생성이나 DNA repair, 더 나아가 세포분열의 기능이 감소하는 등 세포가 damage을 받음을 알 수 있었다. ER stress에 관련된 전사조절인자로는 FOX04, AP-1, FOX03, HNF4, IRF-1, GATA 등의 전사조절인자들이 ER stress에 의해 발현이 증가하는 유전자들의 promoter에 공통적으로 존재하였으며, E2F, Nrf-1, Elk-1, YY1, CREB, MTF-1, STAT-1, ATF 등의 전사인자들이 발현이 감소하는 유전자들의 promoter에서 공통적으로 존재하여, 이들의 전사인자들이 ER stress에 의한 유전자의 발현조절에 중요한 역할을 하는 전사조절인자임을 알 수 있었다.

• Asian Pacific Journal of Cancer Prevention
• /
• 제14권8호
• /
• pp.4553-4557
• /
• 2013

Objective: The purpose of this study was to identify genes related to bladder cancer with samples from normal and disease cases by microarray chip. Methods: After downloading the gene expression profile GSE3167 from Gene Expression Omnibus database which includes 50 bladder samples, comprising 9 normal and 41 disease samples, differentially expressed genes were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Firstly, molecular functions, biological processes and cell component analysis were researched by software Gestalt. Then, software String was used to search interaction relationships among differentially expressed genes, and hub genes of the network were selected. Finally, by using plugins of software Cytoscape, Mcode and Bingo, module analysis of hub-genes was performed. Results: A total of 221 genes were identified as differentially expressed by comparing normal and disease bladder samples, and a network as well as the hub gene C1QBP was obtained from the network. The C1QBP module had the closest relationship to production of molecular mediators involved in inflammatory responses. Conclusion: We obtained differentially expressed genes of bladder cancer by microarray, and both PRDX2 and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses. From knowledge of inflammatory responses and cancer, our results showed that, the hub gene and its module could induce inflammation in bladder cancer. These related genes are candidate bio-markers for bladder cancer diagnosis and might be helpful in designing novel therapies.

• The Korean Journal of Physiology and Pharmacology
• /
• 제10권5호
• /
• pp.263-271
• /
• 2006

Since astrocytes were shown to play a central role in maintaining neuronal viability both under normal conditions and during stress such as ischemia, studies of the astrocytic response to stress are essential to understand many types of brain pathology. The micro array system permitted screening of large numbers of genes in biological or pathological processes. Therefore, the gene expression patterns in the in vitro model of astrocytes following exposure to oxygen-glucose deprivation (OGD) were evaluated by using the micro array analysis. Primary astrocytic cultures were prepared from postnatal Swiss Webster mice. The cells were exposed to OGD for 4 hrs at $37^{\circ}C$ prior to cell harvesting. From the cultured cells, we isolated mRNA, synthesized cDNA, converted to biotinylated cRNA and then reacted with GeneChips. The data were normalized and analyzed using dChip and GenMAPP tools. After 4 hrs exposure to OGD, 4 genes were increased more than 2 folds and 51 genes were decreased more than 2 folds compared with the control condition. The data suggest that the OGD has general suppressive effect on the gene expression with the exception of some genes which are related with ischemic cell death directly or indirectly. These genes are mainly involved in apoptotic and protein translation pathways and gap junction component. These results suggest that microarray analysis of gene expression may be useful for screening novel molecular mediators of astrocyte response to ischemic injury and making profound understanding of the cellular mechanisms as a whole. Such a screening technique should provide insights into the molecular basis of brain disorders and help to identify potential targets for therapy.

• 동의생리병리학회지
• /
• 제20권4호
• /
• pp.853-860
• /
• 2006

This study was performed to investigate genes which are differently expressed in human blood by administrating of OLT-2. OLT-2 was medical precipitation composed of three medicinal herbs, Ginseng Radix, Astragali Radix, Glycyrrhizae Radix, and anti-leukemia effect of it was evaluated from Byung Hun Jeon of Wonkwang University this study was approved by Institutional Review Board of Korea Institute of Oriental Medicine (Taejeon, Korea) and four male subjects participated in this study. Gene expressions were evaluated by cDNA chip, in which 24,000 genes were spotted. Hierarchical cluster and biological process against the genes, which expression changes were more than 1.6 fold, were constructed by cluster 3.0 providing Stanford University and EASE(http://apps1 .maid.nih.gov/DAVID). Five groups were clustered according to their expression patterns. Group A contained gene decreased by OLT-2 and increased genes by OLT-2 were involved in Group B, C, D. In biological process, expression of genes involved in cytokine or cell calcium signaling, such as interleukin 18 and G-protein beta 4 were increased, but protein tyrosine phosphatase receptor type c, which function is cell adhesion between antigen-presenting cell and T or B-cell, was decreased by OLT-2. This study provides the most comprehensive available survey of gene expression changes in response to anti-leukemia effect of OLT-2 in human blood.

• 생명과학회지
• /
• 제22권3호
• /
• pp.366-372
• /
• 2012

본 연구는 한우 유전체 전장에 존재하는 고밀도 단일염기다형을 DNA chip을 이용하여 각각의 유전자형을 구명하고, 동일염색체 내에 존재하는 각 표지인자쌍의 연관불평형을 성 염색체를 제외한 모든 상염색체에서 추정하여 물리적 거리별 연관불평형의 정도를 확인하고 이러한 결과를 이용하여 한우 집단의 유효집단 크기를 추정하기 위하여 실시하였다. 한우개량사업소에서 2005년부터 2008년까지 후대검정에 공시된 후보종모우 및 후대 검정우 288두에 대해 혈액을 채취하고 Bovine SNP 50 DNA Chip을 이용하여 유전자형을 분석하였으며, 총 51,582 표지인자 중 결측률이 10% 이상인 표지인자 1개 및 다형성이 없는 표지인자 10,730개에 대해 사전제거를 실시하고 남은 40,851개의 SNP표지인자를 본 분석에 활용하였다. 연구 결과, 성 염색체를 제외한 상 염색체의 총 SNP표지인자의 길이는 2,541.6 Mb였으며, 염색체별 평균 SNP표지인자간 거리는 0.55에서 0.74로 분포하였으며, EM알고리즘을 이용하여 염색체별 연관불평형을 추정해 보았을 때, 기존의 보고된 연구와 유사하게 표지인자간 거리가 짧을수록 높게 나타나는 지수형태의 그래프를 나타냈으며, SNP표지인자간 거리에 따른 $r^2$를 보면, 0 Mb에서 0.1 Mb일 때 0.136, 0.1-0.2 Mb에서 0.06로 나타났다. Luo (1998)의 연구결과를 한우에 적용시켰을 때, 전체분산의 5%이상 설명하는 양적형질좌위 발굴을 위해서 약 2,000두의 표현형 자료가 필요할 것으로 사료되었다. 또한 한우의 세대별 유효집단 크기에 대해 추정해 본 결과, 현재 한우의 유효집단크기는 84두로 추정되었고, 지금으로부터 약 50세대 이전의 유효집단 크기는 1,150두로 추정되었다. 가축에서 인공수정이 도입(1960년대)된 이 후 개량의 가속화로 인해 한우의 유효집단 크기가 급격히 감소한 것으로 사료되었다.

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

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

• 생명과학회지
• /
• 제20권4호
• /
• pp.584-588
• /
• 2010

Clusterin은 Apolipoprotein J 등으로도 불리우기도 하는데 이 유전자의 발현이 동맥경화의 진행에 영향을 미치며[4], 관상동맥질환과 같은 혈관질환에도 중요한 역할을 하는 것으로 보고되어 있다[9,10,18] 최근 연구결과에 따르면, clusterin 유전자 다형성 중 10580 C>A, 10613 A>G이 아프리카인에게서 HDL-C의 serum level에 영향을 미치며, 이들 변이가 African-American에게서 Caucasian보다는 드물게 나타나지만, Hispanic에게서는 빈번하게 일어나는 것으로 보고되어 있다[11]. 또 다른 연구에서는 11개의 유전자 다형성을 조사한 결과 -4453G >T, 4183 A>G, 5608 C>T 는 상관관계가 없는 것으로 나타났으나, 6316 delT 유전자 다형성은 상관관계가 있는 것으로 보고되었다[8]. 본 연구에서는 관상동맥질환 환자군과 대조군을 각각 100명으로 하여 한국인에서 clusterin 유전자 다형성을 조사하였고, 특히 -4453 T>G에서 유의한 차이를 보였다. 이는 이전의 연구결과[8]와는 다소 차이가 있는데, Miwa 등의 결과에 따르면 일본인에게서는 6316 delT가 4183 A>G 다형성보다 동맥경화와 상관관계가 크다고 보고되었으나, 본 연구결과를 분석해보면 5608 C>T 는 상관관계가 없었으며, -4453 T>G 다형성만 상관관계를 가지는 것으로 나타났다. 이러한 차이를 보이는 원인은 정확하게 지적할 수는 없으나, 다형성이 미치는 영향력이 서로 다른 유전적 그리고 환경적인 요인의 차이에 의해서 일어나는 것으로 추정된다. 따라서 본 연구결과의 의의를 확인하기 위하여서는 대상 환자 수와 대조군을 늘리고 clusterin 유전자의 여러 다형성에 대한 추가적인 연구를 할 필요가 있을 것으로 판단된다.