• Genomics & Informatics
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• v.4 no.3
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• pp.97-102
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• 2006

In acute leukemia patients, several successful methods of expression profiling have been used for various purposes, i.e., to identify new disease class, to select a therapeutic target, or to predict chemo-sensitivity and clinical outcome. In the present study, we tested the peripheral blood of 47 acute leukemia patients in an attempt to identify differentially expressed genes in AML and ALL using a Korean-made 10K oligo-nucleotide microarray. Methods: Total RNA was prepared from peripheral blood and amplified for microarray experimentation. SAM (significant analysis of microarray) and PAM (prediction analysis of microarray) were used to select significant genes. The selected genes were tested for in a test group, independently of the training group. Results: We identified 345 differentially expressed genes that differentiated AML and ALL patients (FWER<0.05). Genes were selected using the training group (n=35) and tested for in the test group (n=12). Both training group and test group discriminated AML and ALL patients accurately. Genes that showed relatively high expression in AML patients were deoxynucleotidyl transferase, pre-B lymphocyte gene 3, B-cell linker, CD9 antigen, lymphoid enhancer-binding factor 1, CD79B antigen, and early B-cell factor. Genes highly expressed in ALL patients were annexin A 1, amyloid beta (A4) precursor protein, amyloid beta (A4) precursor-like protein 2, cathepsin C, lysozyme (renal amyloidosis), myeloperoxidase, and hematopoietic prostaglandin D2 synthase. Conclusion: This study provided genome wide molecular signatures of Korean acute leukemia patients, which clearly identify AML and ALL. Given with other reported signatures, these molecular signatures provide a means of achieving a molecular diagnosis in Korean acute leukemia patents.

• Journal of Pharmacopuncture
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• v.9 no.2
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• pp.39-47
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• 2006

Objective : It has long been known about the anticancer effect of GRR-HAS, however, it has not been systemically determined the differentially regulated genes by GRR-HAS in cancer cells. The purpose of this study is to screen the GRR-HAS mediated differentially expressed genes in cancer cells such as SNU484 gastric cancer cell lines. Oligonucleotide microarray approache was employed to screen the differential expression genes. Methods : GRR-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of GRR-HAS(0.1, 0.5, 1.5, 10, 20mg/ml) for 24 h. Cell toxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with 1.5mg/ml of GRR-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide Genechip (Human genome Ul33 Plus 2.0., Affimatrix Co.). Results : It has no cytotoxic effects on both HepG2 and SNU484 cells in all concentrations(0.1, 0.5, 1.5, 10, 20mg/ml). In oligonucleotide microarray assay, in SNU484 cells, the number of more than twofold up-regulated genes was 346. The number of more than twofold down-regulated genes was 9. Discussion : This study showed the comprehensive gene expression analysis using oligonucleotide microarray for the screening of GRR-HAS mediated differentially regulated genes. These results will provide a better application of GRR-HAS in cancer field and drug target development.

• BMB Reports
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• v.40 no.2
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• pp.226-231
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• 2007

Housekeeping genes are widely used as internal controls in a variety of study types, including real time RT-PCR, microarrays, Northern analysis and RNase protection assays. However, even commonly used housekeeping genes may vary in stability depending on the cell type or disease being studied. Thus, it is necessary to identify additional housekeeping-type genes that show sample-independent stability. Here, we used statistical analysis to examine a large human microarray database, seeking genes that were stably expressed in various tissues, disease states and cell lines. We further selected genes that were expressed at different levels, because reference and target genes should be present in similar copy numbers to achieve reliable quantitative results. Real time RT-PCR amplification of three newly identified reference genes, CGI-119, CTBP1 and GOLGAl, alongside three well-known housekeeping genes, B2M, GAPD, and TUBB, confirmed that the newly identified genes were more stably expressed in individual samples with similar ranges. These results collectively suggest that statistical analysis of microarray data can be used to identify new candidate housekeeping genes showing consistent expression across tissues and diseases. Our analysis identified three novel candidate housekeeping genes (CGI-119, GOLGA1, and CTBP1) that could prove useful for normalization across a variety of RNA-based techniques.

• Environmental Analysis Health and Toxicology
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• v.20 no.4 s.51
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• pp.327-332
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• 2005

장기간 노출 시 발암 등 인체 유해성을 갖는 환경유래 내분비장애물질(endocrine disrupting chemicals, EDCs)에 대한 선택적이고 민감한 노출지표를 개발하기 위하여 본 연구에서는 DNA microarray를 이용하였다. 피험자는 아직 특별한 질환을 갖지 않는 18세 이상 연령, 성을 맞춘 EDCs고농도 노출군(N = 16)과 저농도군(N = 16)으로 구성되었다. 노출정도 구분은 10년 이상 거주지가 K산업폐기물 소각장과 2.5 km 반경 내, 외 인지에 따라 고노출군,저노출군으로 구분하였다. 피험자의 말초혈에서 total RNA를 분리, 각 군당 B인씩 pool로 cDNA를 합성하여 oligonucleotide DNA 칩에 적용하였다. 유전자발현의 차이를 GenePixPro 4.0 software를 이용하여 분석하였다. 총 3장의 칩을 이용하여 공통적으로 저노출군보다 고노출군에서 2배 이상 발현의 증가를 보인 유전자는 plasminogen activator(PLAT)등 12종이 관찰되었고, l/2이하로 발현의 감소를 보인 유전자는 kallikrein 3 (KLK3)등 29종이었다. 이 들 유전자는 PLAT등 면역계 반응에 관여하는 유전자 및 apoptosis, transport, G protein, chromatin, 암화, 발생 (development), 대사 등에 관여하는 유전자들이었다. 그러므로 KLK3등 본 연구에서 발굴한 유전자는 향후 확대된 인구에서 본 연구 결과의 확인을 통하여 EDCs특이적 노출지표로써, 나아가 암 등 EDCs관련 질병의 기전 및 병인학을 구명하는데 이용가치가 높다고 사료된다.

• International Journal of Industrial Entomology and Biomaterials
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• v.23 no.1
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• pp.137-141
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• 2011

A previous data was provided information for tissuespecific expression genes by means of whole-genome oligonucleotide microarray in the silkworm. We analyzed the tissue-specific expression patterns in the hemocyte tissue on 5 days of 5th instar larvae during the development of $B.$ $mori$. Total 5 candidates pick out from the $Bombyx$ $mori$ Microarray Database (BmMDB; http://silkworm.swu.edu.cn/microarray). To verify the hemocyte-specific expression, we analyzed by semi-quantitative and real-time quantitative RT-PCR using the highly expressed endogenous $Actin$ RNA as an intrinsic reference. In this study, we confirmed that one gene-sw17255- out of 5 candidates expressed in the hemocyte tissue, which was consistent with the previous data. Circulating hemocytes in the body fluid of the $B.$ $mori$ are most powerful target organ for producing biomaterials. We need further studies to find hemocyte-specific promoter region from sw17255 gene. Finally, this result can be applied in creating transgenic silkworms as a biomedical insect.

• Journal of Embryo Transfer
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• v.30 no.1
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• pp.17-21
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• 2015

Alteration in ion channel or transporter expression levels affects cell volume which is produced by movement of water and ion across the plasma membrane. In particular, aquaporin (AQP) channels among ion channels play a crucial role in movement of water across the cell membrane. This study was performed to identify whether AQP expression is changed in bovine follicular cystic follicles using microarray, RT-PCR and Western blotting analyses. In microarray data, AQP4 expression was decreased, whereas AQP7 was increased in cystic follicles. Additional experiments were focused on the AQP7 expression increased in cystic follicles. The microarray data was confirmed by semi-quantitative polymerase chain reaction (PCR) and Western blot analysis. AQP7 mRNA and protein expressions were significantly increased in the cystic follicles (p<0.05). Application of estrogen ($10{\mu}g/ml$) to bovine ovarian cells showed a trend of increase in AQP7 expression. From these results, we suggest that the increase in AQP7 expression in cystic follicles may play an important role in movement of water in bovine ovary. In addition, AQP7, a aquaglyceroporin permeating water and glycerol, could be a good target in development of methods for the cryopreservation of bovine ovary.

• BMB Reports
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• v.43 no.5
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• pp.344-348
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• 2010

Messenger ribonucleoprotein particles (mRNPs) are used to transport mRNAs along neuronal dendrites to their site of translation. Staufen2 is an mRNA-binding protein expressed in the cell bodies and cellular processes of different brain cells. It is notably involved in the transport of dendritic mRNAs along microtubules. Its knockdown expression was shown to change spine morphology and impair synaptic functions. However, the identity of Staufen2-bound mRNAs in brain cells is still completely unknown. As a mean to identify these mRNAs, we immunoprecipitated Staufen2-containing mRNPs from embryonic rat brains and used a genome wide approach to identify Staufen2-associated mRNAs. The genome wide approach identified 1780 mRNAs in Staufen2-containing mRNPs that code for proteins involved in cellular processes such as post-translational protein modifications, RNA metabolism, intracellular transport and translation. These results represent an additional and important step in the characterization of Staufen2- mediated neuronal functions in rat brains.

• Journal of Applied Biological Chemistry
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• v.55 no.4
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• pp.227-234
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• 2012

We observed that oil began to accumulate at 25 seed days after flowering (DAF) and reached the maximum potential at 35 seed DAF of oilseed rape, and the greatest weight of 100 seeds was obtained at 35 seed DAF. To survey a broad analysis of gene expression in developing embryos of Brassica napus, the Bn 300k microarray have been constructed. The Bn 300k Microarrary was designed from 80,696 unigenes clustered from 543,448 ESTs and 780 cDNA at NCBI. These arrays have been hybridized in a series of experiments with probes derived from seeds and leaf of B. napus. Approximately 8.5% of the 7,000 genes were expressed as ratios 2-fold higher in seed (25 DAF) than leaves and 0.4% at ratios 10. Also we observed that storage and cell differentiation-related genes were highly expressed at 10 DAF, whereas energy-related genes including fatty acid metabolism were increased up depending on seed maturation using Microarray, which was confirmed by reverse transcriptase polymerase chain reaction. These results suggest that B. napus arrays provide a very useful data set of seed-specific expression that can be further analyzed by examination of the promoter regions of these genes and help our understanding of the complex regulatory network in developing seeds.

• International Neurourology Journal
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• v.22 no.4
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• pp.237-245
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• 2018

Purpose: Presenilins are functionally important components of ${\gamma}$-secretase, which cleaves a number of transmembrane proteins. Manipulations of PSEN1 and PSEN2 have been separately studied in Alzheimer disease (AD) and cancer because both involve substrates of ${\gamma}$-secretase. However, numerous clinical studies have reported an inverse correlation between AD and cancer. Interestingly, AD is a neurodegenerative disorder, whereas cancer is characterized by the proliferation of malignant cells. However, this inverse correlation in the PSEN double-knockout (PSEN dKO) mouse model of AD has been not elucidated, although doing so would shed light onto the relationship between AD and cancer. Methods: To investigate the inverse relationship of AD and cancer under conditions of PSEN loss, we used the hippocampus of 7-month-old and 18-month-old PSEN dKO mice for a microRNA (miRNA) microarray analysis, and explored the tumorsuppressive or oncogenic role of differentially-expressed miRNAs. Results: The total number of miRNAs that showed changes in expression level was greater at 18 months of age than at 7 months. Most of the putative target genes of the differentially-expressed miRNAs involved Cancer pathways. Conclusions: Based on literature reviews, many of the miRNAs involved in Cancer pathways were found to be known tumorsuppressive miRNAs, and their target genes were known or putative oncogenes. In conclusion, the expression levels of known tumor-suppressive miRNAs increased at 7 and 18 months, in the PSEN dKO mouse model of AD, supporting the negative correlation between AD and cancer.

• Biomolecules & Therapeutics
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• v.18 no.4
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• pp.411-419
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• 2010

Korean mistletoe has a variety of biological effects, such as immunoadjuvant activities. This study investigates the effects of Korean mistletoe lectin (Viscum album L. var. coloratum agglutinin, VCA) on human T lymphocytes to determine whether VCA acts as an immunomodulator. Purified human T-lymphocytes were cultured with VCA and RNA from each point was analyzed using Affymetrix human genome chips containing 22,500 probe sets which represents more than 18,000 transcripts derived from 14,500 human genes. As a result, there was a striking upregulation of genes coding for chemokines. Seventeen genes out of 50 coding for proteins with chemokine activity were upregulated including CXCL9 and IL-8 which are related to the treatment of cancer. In addition, 28 cytokine genes were upregulated including IL-1, IL-6, IL-8, IFN-$\gamma$, and TNF-$\alpha$. Taken together, the data suggest that Korean mistletoe lectin, in parallel with European mistletoe, has an ability to modulate human T cell function.