• Journal of Life Science
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• v.19 no.9
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• pp.1294-1298
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• 2009

To investigate whether isoflavone genistein and daidzein could affect cancer cell viability, human colorectal HCT116 cells were incubated with genistein or daidzein in a dose-dependent manner. Genistein decreased cancer cell viability in a dose-dependent manner, whereas daidzein did not show dramatic cytotoxic effects. We also found that 71 genes were up-regulated more than 2-fold, whereas 64 genes were down-regulated more than 2-fold with 24 hr of $50{\mu}M$ genistein treatment by our previous microarray data. Among the up-regulated genes, we selected 3 genes (DKK1, ATF3 and NAG-1) and performed RT-PCR to confirm microarray data. The results of RT-PCR were highly correlated with those of the microarray experiment. In addition, we investigated whether a combination treatment of genistein and daidzein could affect cancer cell viability. Surprisingly, the combination treatment did show synergistic cytotoxic effects detected by MTS assay. The results of RT-PCR and real-time PCR indicate that a combination of genistein and daidzein can synergistically induce NAG-1 expression in HCT116 cells. This result implies that NAG-1 induction is highly associated with synergistic cytotoxic effects induced by a combination treatment of genistein and daidzein. Overall, these results may provide a clue in explaining the anti-cancer activity of soy bean in human colorectal cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8135-8140
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• 2016

Background: Cell cycle regulatory proteins are suitable targets for cancer therapeutic development since genetic alterations in many cancers also affect the functions of these molecules. Strobilanthes crispus (S. crispus) is traditionally known for its potential benefits in treating various ailments. We recently reported that an active sub-fraction of S. crispus leaves (SCS) caused caspase-dependent apoptosis of human breast cancer MCF-7 and MDA-MB-231 cells. Materials and Methods: Considering the ability of SCS to also promote the activity of the antiestrogen, tamoxifen, we further examined the effect of SCS in modulating cell cycle progression and related proteins in MCF-7 and MDA-MB-231 cells alone and in combination with tamoxifen. Expression of cell cycle-related transcripts was analysed based on a previous microarray dataset. Results: SCS significantly caused G1 arrest of both types of cells, similar to tamoxifen and this was associated with modulation of cyclin D1, p21 and p53. In combination with tamoxifen, the anticancer effects involved downregulation of $ER{\alpha}$ protein in MCF-7 cells but appeared independent of an ER-mediated mechanism in MDA-MB-231 cells. Microarray data analysis confirmed the clinical relevance of the proteins studied. Conclusions: The current data suggest that SCS growth inhibitory effects are similar to that of the antiestrogen, tamoxifen, further supporting the previously demonstrated cytotoxic and apoptotic actions of both agents.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.165-196
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• 2001

DNA chip 또는 microarray는 다수의 유전자 또는 유전자 조각을 (보통 수천내지 수만 개)칩상에 고정시켜 놓고 DNA hybridization 반응을 이용하여 유전자들의 발현 양상을 분석할 수 있는 기술이다. 이러한 high-throughput기술은 예전에는 생각하지 못했던 여러가지 분자생물학의 문제에 대한 해답을 제시해 줄 수 있을 뿐 만 아니라, 분자수준에서의 질병 진단, 신약 개발, 환경 오염 문제의 해결 등 그 응용 가능성이 무한하다. 이 기술의 실용적인 적용을 위해서는 DNA chip을 제작하기 위한 하드웨어/웻웨어 기술 외에도 이러한 데이터로부터 최대한 유용하고 새로운 지식을 창출하기 위한 bioinformatics 기술이 핵심이라고 할 수 있다. 유전자 발현 패턴을 데이터마이닝하는 문제는 크게 clustering, classification, dependency analysis로 구분할 수 있으며 이러한 기술은 통계학과인공지능 기계학습에 기반을 두고 있다. 주로 사용된 기법으로는 principal component analysis, hierarchical clustering, k-means, self-organizing maps, decision trees, multilayer perceptron neural networks, association rules 등이다. 본 세미나에서는 이러한 기본적인 기계학습 기술 외에 최근에 연구되고 있는 새로운 학습 기술로서 probabilistic graphical model (PGM)을 소개하고 이를 DNA chip 데이터 분석에 응용하는 연구를 살펴본다. PGM은 인공신경망, 그래프 이론, 확률 이론이 결합되어 형성된 기계학습 모델로서 인간 두뇌의 기억과 학습 기작에 기반을 두고 있으며 다른 기계학습 모델과의 큰 차이점 중의 하나는 generative model이라는 것이다. 즉 일단 모델이 만들어지면 이것으로부터 새로운 데이터를 생성할 수 있는 능력이 있어서, 만들어진 모델을 검증하고 이로부터 새로운 사실을 추론해 낼 수 있어 biological data mining 문제에서와 같이 새로운 지식을 발견하는 exploratory analysis에 적합하다. 또한probabilistic graphical model은 기존의 신경망 모델과는 달리 deterministic한의사결정이 아니라 확률에 기반한 soft inference를 하고 학습된 모델로부터 관련된 요인들간의 인과관계(causal relationship) 또는 상호의존관계(dependency)를 분석하기에 적합한 장점이 있다. 군체적인 PGM 모델의 예로서, Bayesian network, nonnegative matrix factorization (NMF), generative topographic mapping (GTM)의 구조와 학습 및 추론알고리즘을소개하고 이를 DNA칩 데이터 분석 평가 대회인 CAMDA-2000과 CAMDA-2001에서 사용된cancer diagnosis 문제와 gene-drug dependency analysis 문제에 적용한 결과를 살펴본다.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6375-6378
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• 2012

Background: Small-cell lung cancer (also known as SCLC) is an aggressive form and untreated patients generally die within about 3 months. To obtain further insight into mechanism underlying malignancy with this cancer, an miRNA synergistic regulatory network was constructed and analyzed in the present study. Method: A miRNA microarray dataset was downloaded from the NCBI GEO database (GSE27435). A total of 546 miRNAs were identified to be expressed in SCLC cells. Then a miRNA synergistic network was constructed, and the included miRNAs mapped to the network. Topology analysis was also performed to analyze the properties of the synergistic network. Consequently, we could identified constitutive modules. Further, common target genes of each module were identified with CFinder. Finally, enrichment analysis was performed for target genes. Results: In this study, a miRNA synergistic network with 464 miRNAs and 2981 edges was constructed. According to the topology analysis, the topological properties between the networks constructed by LC related miRNAs and LC unrelated miRNAs were significantly different. Moreover, a module cilque0 could be identified in our network using CFinder. The module included three miRNAs (hsa-let-7c, hsa-let-7b and hsa-let-7d). In addition, several genes were found which were predicted to be common targets of cilque0. The enrichment analysis demonstrated that these target genes were enriched in MAPK signaling pathways. Conclusions: Although limitations exist in the current data, the results uncovered here are important for understanding the key roles of miRNAs in SCLC. However, further validation is required since our results were based on microarray data derived from a small sample size.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.4
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• pp.1783-1789
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• 2014

Background: The EMSY gene encodes a BRCA2-binding partner protein that represses the DNA repair function of BRCA2 in non-hereditary breast cancer. Although amplification of EMSY gene has been proposed to have prognostic value in breast cancer, no data have been available concerning EMSY tissue expression patterns and its associations with clinicopathological features. Materials and Methods: In the current study, we examined the expression and localization pattern of EMSY protein by immunohistochemistry and assessed its prognostic value in a well-characterized series of 116 unselected breast carcinomas with a mean follow up of 47 months using tissue microarray technique. Results: Immunohistochemical expression of EMSY protein was detected in 76% of primary breast tumors, localized in nuclear (18%), cytoplasmic (35%) or both cytoplasmic and nuclear sites (23%). Univariate analysis revealed a significant positive association between EMSY expression and lymph node metastasis (p value=0.045) and larger tumor size (p value=0.027), as well as a non-significant relation with increased risk of recurrence (p value=0.088), whereas no association with patients' survival (log rank test, p value=0.482), tumor grade or type was observed. Conclusions: Herein, we demonstrated for the first time the immunostaining pattern of EMSY protein in breast tumors. Our data imply that EMSY protein may have impact on clinicipathological parameters and could be considered as a potential target for breast cancer treatment.

• Molecules and Cells
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• v.38 no.4
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• pp.304-311
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• 2015

Most follicles in the mammalian ovary undergo atresia. Granulosa cell apoptosis is a hallmark of follicle atresia. Our previous study using a microRNA (miRNA) microarray showed that the let-7 microRNA family was differentially expressed during follicular atresia. However, whether the let-7 miRNA family members are related to porcine (Sus scrofa) ovary follicular apoptosis is unclear. In the current study, real-time quantitative polymerase chain reaction showed that the expression levels of let-7 family members in follicles and granulosa cells were similar to our microarray data, in which miRNAs let-7a, let-7b, let-7c, and let-7i were significantly decreased in early atretic and progressively atretic porcine ovary follicles compared with healthy follicles, while let-7g was highly expressed during follicle atresia. Furthermore, flow cytometric analysis and Hoechst33342 staining demonstrated that let-7g increased the apoptotic rate of cultured granulosa cells. In addition, let-7 target genes were predicted and annotated by TargetScan, PicTar, gene ontology and Kyoto encyclopedia of genes and genomes pathways. Our data provide new insight into the association between the let-7 miRNA family in granulosa cell programmed death.

• Molecules and Cells
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• v.37 no.11
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• pp.795-803
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• 2014

To withstand ever-changing environmental stresses, plants are equipped with phytohormone-mediated stress resistance mechanisms. Salt stress triggers abscisic acid (ABA) signaling, which enhances stress tolerance at the expense of growth. ABA is thought to inhibit the action of growth-promoting hormones, including brassinosteroids (BRs). However, the regulatory mechanisms that coordinate ABA and BR activity remain to be discovered. We noticed that ABA-treated seedlings exhibited small, round leaves and short roots, a phenotype that is characteristic of the BR signaling mutant, brassinosteroid insensitive1-9 (bri1-9). To identify genes that are antagonistically regulated by ABA and BRs, we examined published Arabidopsis microarray data sets. Of the list of genes identified, those upregulated by ABA but downregulated by BRs were enriched with a BRRE motif in their promoter sequences. After validating the microarray data using quantitative RT-PCR, we focused on RD26, which is induced by salt stress. Histochemical analysis of transgenic Arabidopsis plants expressing RD26pro:GUS revealed that the induction of GUS expression after NaCl treatment was suppressed by co-treatment with BRs, but enhanced by co-treatment with propiconazole, a BR biosynthetic inhibitor. Similarly, treatment with bikinin, an inhibitor of BIN2 kinase, not only inhibited RD26 expression, but also reduced the survival rate of the plant following exposure to salt stress. Our results suggest that ABA and BRs act antagonistically on their target genes at or after the BIN2 step in BR signaling pathways, and suggest a mechanism by which plants fine-tune their growth, particularly when stress responses and growth compete for resources.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.320-324
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• 2018

Chunkookjang, fermented soybean is rich in diverse oligopeptides which derived from cleavage of soybean proteins during fermentation. Microarray data containing differently expressed genes in breast cancer cells treated with fermented soybean extract and well known breast cancer metastasis markers were combined, and a new network was constructed. It is used to check interactions between the marker proteins and the differently expressed genes. Based on the network analysis, PLAU (plasminogen activator, urokinase, uPA) and ERBB2 (epidermal growth factor receptor 2) are chosen as possible metastasis genes. We treated breast cancer MCF7 cells with fermented soybean extract and measured expression levels of PLAU and ERBB2. Fermented soybean extract suppressed PLAU and ERBB2 expressions conspicuously. In the cancer cells treated with fermented soybean extracts, an inflammation marker, NO production was also reduced. It will be interesting to find specific peptides to suppress PLAU and ERBB2 expressions in human breast cancer cells.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.281-283
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• 2005

Extraction of biologically meaningful data and their validation are very important for toxicogenomics study because it deals with huge amount of heterogeneous data. BINGO is an annotation mining tool for biological interpretation of gene groups. Several statistical modeling approaches using Gene Ontology (GO) have been employed in many programs for that purpose. The statistical methodologies are useful in investigating the most significant GO attributes in a gene group, but the coherence of the resultant GO attributes over the entire group is rarely assessed. BINGO complements the statistical methods with graph-theoretic measures using the GO directed acyclic graph (DAG) structure. In addition, BINGO visualizes the consistency of a gene group more intuitively with a group-based GO subgraph. The input group can be any interesting list of genes or gene products regardless of its generation process if the group is built under a functional congruency hypothesis such as gene clusters from DNA microarray analysis.

• Journal of Embryo Transfer
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• v.24 no.1
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• pp.57-64
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• 2009

This study was carried out to investigate expression of apoptosis-related differentially expressed gene (DEG) in ovaries of Korean cattle with follicular and luteal cysts and to identify the relationship between cyst and apoptosis using microarray, real-time PCR, TUNEL staining, and Western blot analysis. Microarray data showed that PIK3R2 and AKT1 were significantly up-regulated in follicular cyst, and TNF-RAF2, PRLR, FOXL2, STK4, and COL4A3 were up-regulated whereas INHA, CIDEB, BCL10, and FASLG were down-regulated in luteal cyst. Real-time PCR was performed to validate DEGs altered in luteal cyst. Of nine DEGs, four DEGs down-regulated in luteal cyst showed a positive corelation between microarray data and real-time PCR data. In this study, we focused on INHA, among many DEGs, which was highly down-regulated in both follicular and luteal cysts. Real-time PCR and micro array data showed that INHA was down-regulated by 12.3-fold and by 1.4-fold, respectively, in the bovine follicular cyst. TUNEL assay and Western blot analysis for ERK, JNK, p38, PI3K, and Akt, which were used to detect whether apoptosis is occurred, showed no significant changes in cystic ovaries (p>0.05). In the expression and activity of caspase-3, Bax, Bel-2, and Bel-xL, there was no significant changes between follicular cystic ovary and normal ovary. Rather, the expression levels of PI3K and p-Akt were decreased in follicular cystic ovary. These results suggest that deficiency of apoptosis in cystic ovary is associated with decreased expression of apoptotic effectors.