• 한국환경성돌연변이발암원학회지
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• 제22권1호
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• pp.54-59
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• 2002

We have used cDNA microarray hybridization to identify gene regulated in response to gamma-irradiation in U-937 cell. The cDNA-chip was composed entirely of 1,000 human cancer related gene including apoptosis and angiogenesis etc. In gamma-irradiated U-937 cell, highly charged protein, ribosomal protein L32, four and a half LIM domains 3, lipocalin 2 (oncogene 24p3) and interleukin 15, ataxia telangiectasia mutated (includes complementation groups A, C and D) genes showed increased level of its transcription, and cell division cycle 25A, dihydrofolate reductase, topoisomerase (DNA) II beta(180kD), kinase suppressor of ras and strarigin genes showed reduced level of its transcription compared to untreated U-937 cell. The significant change of level of transcription was not found in well-known ionizing radiation(IR)-responsive gene, such as transcription factor TP53 and p53 related gene, except ataxia telangiectasia mutated gene.

• Asian Pacific Journal of Cancer Prevention
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• 제14권10호
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• pp.6089-6094
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• 2013

Berberine, a common isoquinoline alkaloid, has been shown to possess anti-cancer activities. However, the underlying molecular mechanisms are still not completely understood. In the current study, we investigated the effects of berberine on cell growth, colony formation, cell cycle distribution, and whether it improved the anticancer efficiency of cisplatin and doxorubicin in human breast cancer estrogen receptor positive (ER+) MCF-7 cells and estrogen receptor negative (ER-) MDA-MB-231 cells. Notably, berberine treatment significantly inhibited cell growth and colony formation in the two cell lines, berberine in combination with cisplatin exerting synergistic growth inhibitory effects. Accompanied by decreased growth, berberine induced G1 phase arrest in MCF-7 but not MDA-MB-231 cells. To provide a more detailed understanding of the mechanisms of action of berberine, we performed genome-wide expression profiling of berberine-treated cells using cDNA microarrays. This revealed that there were 3,397 and 2,706 genes regulated by berberine in MCF-7 and MDA-MB-231 cells, respectively. Fene oncology (GO) analysis identified that many of the target genes were involved in regulation of the cell cycle, cell migration, apoptosis, and drug responses. To confirm the microarray data, qPCR analysis was conducted for 10 selected genes based on previously reported associations with breast cancer and GO analysis. In conclusion, berberine exhibits inhibitory effects on breast cancer cells proliferation, which is likely mediated by alteration of gene expression profiles.

• Asian Pacific Journal of Cancer Prevention
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• 제16권15호
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• pp.6417-6421
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• 2015

Viscum album var (VAV) also known as mistletoe, has long been categorized as a traditional herbal medicine in Asia. In addition to its immunomodulating activities, mistletoe has also been used in the treatment of chronic hepatic disorders in China and Korea. There are numerous reports showing that VAV possesses anti-cancer effects, however influence on human hepatocarcinoma has never been elucidated. In the present study, hot water extracts of VAV was evaluated for its potential anti-cancer effect in vitro. SK-Hep1 cells were treated with VAV (50-400ug/ml) for both 24 and 48 hours then cell viability was measured by cell counting kit-8 (CCK-8). Flow cytometry analysis was used to measure the proportion of SK-Hep1 in the different stages of cell cycle. RT-PCR and Western blot analysis were conducted to measure expression of cell cycle arrest related genes and proteins respectively. VAV dose dependently inhibited the proliferation of SK-Hep1 cells without any cytotoxicity with normal Chang liver cell (CCL-13). Flow cytometry analysis showed that VAV extract inhibited the cell cycle of SK-Hep1 cells via G1 phase arrest. RT-PCR and Western blot analysis both revealed that cyclin dependent kinase 2 (Cdk2) and cyclin D1 gene expression were significantly down regulated while p21 was upregulated dose dependently by VAV treatment. Combined down regulation of Cdk2, Cyclin D1 and up regulation of p21 can result in cell death. These results indicate that VAV showed evidence of anti-cancer activity through G1 phase cell cycle arrest in SK-Hep1 cells.

• BMB Reports
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• 제29권4호
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• pp.359-364
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• 1996

By both in vitro hydroxylamine mutagenesis of the wild type 3-phosphoglycerate kinase gene (PGK) promoter DNA and insertion of the leu2-d gene, we have created yeast expression vectors potentially useful for production of eukaryotic genes in yeast. The guanine (G) to adenine (A) change at the -3 position from the ATG start codon of the PGK promoter-based vector rendered a 6~7 times elevated expression of the adjacent eukaryotic gene, and insertion of the leu2-d gene in the vector containing the mutated PGK promoter further enhanced the expression of the gene. When expression of the AIDS virus HIV1-gagP17 gene in a lacZ fusion form was examined with this new vector, a 15 times higher level of expression than that from the original PGK promoter was observed. Northern and Southern analysis showed that this elevated expression is due to the production of a high copy number of mRNA by leu2-d gene functioning and by efficient translation of the produced mRNA. Thus, the vector that contained the A at the -3 position from the ATG start codon in the promoter region and the leu2-d gene shows increased expression capability and will be potentially useful for production of eukaryotic genes in yeast.

• 한국정보과학회논문지:소프트웨어및응용
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• 제31권12호
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• pp.1591-1601
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• 2004

유전자를 분석하는 방법 중 하나인 클러스터링은 비슷한 기능을 가진 유전자들을 집단화시켜서 유전자 집단의 기능을 분석하는데 이용되고 있다. 유전자들은 다양한 functional family에 속할 수 있기 때문에 각 유전자의 클러스터를 하나로 결정짓는 기존의 클러스터링 방법보다 퍼지 클러스터링 방법이 유전자 클러스터링에 더 적합하다. 본 논문에서는 피지 클러스터 결과를 효과적으로 검증할 수 있는 베이지안 검증 방법을 제안한다. 베이지안 검증 방법은 확률기반의 방법으로 주어진 데이타에 대해 가장 큰 사후확률을 가진 클러스터 분할을 선택한다. 먼저 본 논문에서 제안하는 베이지안 검증 방법과 기존의 대표적인 4가지 퍼지 클러스터 검증 방법들을 4가지 데이타에 대해 퍼지 c-means알고리즘을 대상으로 비교 평가한다. 그리고 발아효모 세포주기 발현 데이타를 클러스터링한 후, 제안하는 방법으로 그 결과를 검증하여 분석한다.

• 동의신경정신과학회지
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• 제26권1호
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• pp.63-78
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• 2015

Objectives: Pinelliae Rhizoma has traditionally been used as an anti-depressant in oriental medicine. This study is to investigate the effect of Pinelliae Rhizoma extract (PRe) on psychological stress in genome wild expression of mice. Methods: After giving physical stress to mice, PRe was orally administered with 100 mg/kg/day for five days. After extracting whole brain tissue from the mice, their genome changes were observed by micorarray analysis method. The genome changes were analyzed by IMAGENE 4.0, TREEVIEW, FatiGo algorithems, BOND database, cytoscape program, etc. Results: 1. PRe administered group were remained at normal level; 60% of increase was shown in expressed genes by physical stress, and 65% of decrease was shown in expressed genes by psychological stress. 2. Genes with increased expression in control group that remained at a normal state in PRe administered group were involved with the gene of a cellular metabolic process on biological process, protein binding on molecular function, and cell part on cell composition. The pathway was found to be cytokin-cytokin receptor interaction. 3. Genes with decreased expression in control group that remained at a normal state in PRe administered group were involved with the gene of a cellular metabolic process on biologiacl detail and coupled ATPaes activity on molecular function. This gene related path was Ubiquintin mediated proteolysis etc. 4. Core node genes analyzed by protein interaction network were Vinculin, Cell sdivision cycle 42 homolog (S. cerevisiae) etc. They played an important role in maintaining cytoskeleton and controlling cell cycle. Conclusions: Several genes were up-regulated and down-regulated in response to psychological stress. The expression of most of the genes that were altered in response to psychological stress was restored to normal levels in PRe treated mice. When the interaction network information was analyzed, the recovery of the core node genes in PRe treated mice indicates that this final set of genes may be the effective target of PRe.

• Molecular & Cellular Toxicology
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• 제2권4호
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• pp.273-278
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• 2006

95 squamous cell lung carcinoma samples (normal tissue: 40 samples, tumor: 55 samples) were analyzed with 8 K cDNA microarray. 1-way ANOVA test was employed to select differentially expressed genes in tumor with FDR<0.01. Among the selected 1,655 genes, final 212 genes were chosen according to the expression fold change and used for following analysis. The expression of up-regulated 64 genes was verified with Reverse Transcription PCR and 10 genes were identified as candidates for SCC markers. In our opinion, those candidates can be exploited as diagnostic or therapeutic purposes. Gene Ontology (GO) based analysis was performed using those 212 genes, and following categories were revealed as significant biological processes: Immune response (GO: 0006955), antigen processing (GO: 0030333), inflammatory response (GO: 0006954), Cell adhesion (GO: 0007155), and Epidermis differentiation (GO: 0008544). Gene set enrichment analysis (GSEA) also carried out on overall gene expression profile with 522 functional gene sets. Glycolysis, cell cycle, K-ras and amino acid biosynthesis related gene sets were most distinguished. These results are consistent with the known characteristics of SCC and may be interconnected to rapid cell proliferation. However, the unexpected results from ERK activation in squamous cell carcinoma gripped our attention, and further studies are under progress.

• 대한한방내과학회지
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• 제26권1호
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• pp.48-59
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• 2005

Objectives : The aim of the study was to evaluate the effect of WS on HepG2 cell cycle and expression of related genes. Methods : The MTT assay, Cell counting analysis, $[^3H]-Thymidine$ Incorporation Assay, Flow cytometric analysis, Quantitative RT-PCR were studied. Results : WS inhibited HepG2 cell proliferation in low concentration$(1-10\;{\mu]g/ml)$ which did not cause direct cytotoxicity, with dose-dependant manner. WS in-hibited DNA synthesis as well. Flow cytometric analysis on the HepG2 cell showed G2/M phase arrest. Conclusion : These results suggest that WS inhibits HepG2 cell proliferation not by the gene regulation but by G2/M phase arrest in the cell cycle. Thus further studies on the effect of WS in G2/M phase regulation are thought to be needed.

• Biomolecules & Therapeutics
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• 제20권3호
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• pp.313-319
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• 2012

In recent years, inhibition of HDACs has emerged as a potential strategy to reverse aberrant epigenetic changes associated with cancer, and several classes of HDAC inhibitors have been found to have potent and specific anticancer activities in preclinical studies. But their precise mechanism of action has not been elucidated. In this study, a novel synthetic inhibitor of HDAC, 3-(4-dimethylamino phenyl)-N-hydroxy-2-propenamide [IN-2001] was examined for its antitumor activity and the underlying molecular mechanisms of any such activity on human breast cancer cell lines. IN-2001 effectively inhibited cellular HDAC activity ($IC_{50}$ = 0.585 nM) inMDA-MB-231 human breast cancer cells. IN-2001 caused a significant dose-dependent inhibition of cell proliferation in estrogen receptor (ER) negative MDA-MB-231human breast cancer cells. Cell cycle analysis revealed that the growth inhibitory effects of IN-2001 might be attributed to cell cycle arrest at $G_0/G_1$ and/or $G_2$/Mphase and subsequent apoptosis in human breast cancer cells. These events are accompanied by modulating several cell cycle and apoptosis regulatory genes such as CDK inhibitors $p21^{WAF1}$ and $p27^{KIP1}$ cyclin D1, and other tumor suppressor genes such as cyclin D2. Collectively, IN-2001 inhibited cell proliferation and induced apoptosis in human breast cancer cells and these findings may provide new therapeutic approaches, combination of antiestrogen together with a HDAC inhibitor, in the hormonal therapy-resistant ER-negative breast cancers. In summary, our data suggest that this histone deacetylase inhibitor, IN-2001, is a novel promising therapeutic agent with potent antitumor effects against human breast cancers.

• Molecules and Cells
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• 제20권1호
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• pp.97-104
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• 2005

To investigate apoptosis in HC11 mammary epithelial cells, we compared the gene expression profiles of actively growing and serum-starved apoptotic cells using a mouse apoptosis gene array and $^{33}P$-labeled cDNA prepared from the RNA of the two cultures. Analysis of the arrays showed that expression of several genes such as clusterin, secreted frizzled related protein mRNA (sFRP-1), CREB-binding protein (CBP), and others was higher in the apoptotic cells whereas expression of certain genes including survivin, cell division cycle 2 homolog A (CDC2), and cyclin A was lower. These expression patterns were confirmed by RT-PCR and/or Northern analyses. We compared the expression of some of these genes in the mouse mammary gland under various physiological conditions. The expression levels of genes (clusterin, CBP, and M6P-R) up-regulated in apoptotic conditions were higher at involution than during lactation. On the other hand, genes (Pin, CDC2) downregulated in apoptotic conditions were relatively highly expressed in virgin and pregnant mice. We conclude that certain genes such as clusterin, sFRP-1, GAS1 and CBP are induced in apoptotic mammary epithelial cells, and others are repressed. Moreover, the apoptosis array is an efficient technique for comparing gene expression profiles in different states of the same cell type.