• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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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.

• Clinical and Experimental Pediatrics
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• v.48 no.2
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• pp.197-203
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• 2005

Purpose : Changes in metalloproteinases(MMP) activity have been demonstrated in several disease states, including rheumatoid arthritis and tumor metastasis. More importantly, increased myocardial MMP activity has been reported to occur in both clinical and experimental forms of dilated cardiomyopathy. There was no report about MMP in adriamycin(ADR)-induced cardiomyopathy. The purpose of this study was to investigate gene expression of MMP and tissue inhibitor of metalloproteinases(TIMP) in ADR-induced cardiomyopathy and clarify the relationship between MMP and cytokines. Methods : Male Sprague-Dawley rats were divided into two groups. The first group was control. The second group was given intraperitoneal injections of ADR(5 mg/kg) twice a week over two weeks. Serum concentrations of MMP, TIMP, interleukin(IL)-6 and tumor necrosis factor(TNF)-${\alpha}$ were measured. RNA extraction was performed from frozen rat hearts. Reverse transcription polymerase chain reaction(RT-PCR) was employed. cDNA Microarray analysis was performed by using a set of 5,184 sequence-verified rat cDNA clones. Results : Serum MMP and TIMP levels were not significantly different between the two groups. IL-6 was $36.8{\pm}2.8pg/mL$ and TNF-${\alpha}$ $2.2{\pm}2.7pg/mL$ in the ADR group. They were significantly higher than in the control group. Serum MMP correlated significantly with TNF-${\alpha}$(r=0.41, P<0.05). There was no gene expression of MMP, IL-6 or TNF-${\alpha}$ in the hearts of both groups. Gene expression of TIMP was significantly depressed in the hearts of the ADR group. Conclusion : These results suggested a potential role for TNF-${\alpha}$ in the regulation of extracellular matrix remodeling in ADR induced cardiomyopathy. Rapid screening of multiple decreased gene expression by DNA chip may be a useful diagnostic test to detect early cardiac injury before developing ADR induced cardiomyopathy.

• Tuberculosis and Respiratory Diseases
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• v.50 no.1
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• pp.29-41
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• 2001

Background : The appearance of multiple-drug-resistant Mycobacterium tuberculosis strains has been seriously compromising successful control of tuberculosis. Rifampin-resistance, caused by mutations in the rpoB gene, can be indicative of multiple-drug-resistance, and its detection is of great importance. The present study aimed to develop an oligonucleotide chip for accurate and convenient screening of drug-resistance. Methods : In order to detect point mutations in the rpoB gene, an oligonucleotide chip was prepared by immobilizing specific probe DNA to a microscopic slide glass by a chemical reaction. The probe DNA that was selected from the 81 bp core region of the rpoB gene was designed to have mutation sites at the center. A total of 17 mutant probes related to rifampin-resistance including 8 rifabutin-sensitive mutant probes were used in this study. For accurate determination, wild type probes were prepared for each mutation position with an equal length, which enabled a direct comparison of the hybridization intensities between the mutant and wild type. Results : Mycobacterial genomic DNA from clinical samples was tested with the oligonucleotide chip and the results were compared with those of the drug-susceptibility test in addition to sequencing and INNO-LiPA Rif. TB kit test in some cases. Out of 15 samples, the oligonucleotide chip results of 13 samples showed good agreement with the rifabutin-sensitivity results. The two samples with conflicting result also showed a discrepancy between the other tests, suggesting such possibilities as existence of mixed strains and difference in drug-sensitivity. Further verification of these samples in addition to more case studies are required before the final evaluation of the oligonucleotide chip can be made. Conlcusion : An oligonucleotide chip was developed for the detection of rpoB gene mutations related to drugsusceptibility. The results to date show the potential for using the oligonucleotide chip for accurate and convenient screening of drug-resistance to provide useful information in antituberculosis drug therapy.

• Journal of Acupuncture Research
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• v.25 no.2
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• pp.11-26
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• 2008

목적 : 홍삼약침(藥鍼)이 고혈당 및 지질대사장애에 미치는 개선효과와 그 기전을 조사하고자 한다. 방법 : 홍삼약침(藥鍼)의 anti-diabetic 활성과 그 기전을 C57BL/KsJ db/db mice를 이용하여 관찰하였다. 실험 동물은 대조군(DC), 홍삼약침(藥鍼)군(RGL, RGH) 및 양성대조군(MET, GPZ, PIO)의 6군으로 나누었다. 홍삼약침(藥鍼)군은 $0.2m{\ell}$의 홍삼약침멸(藥鍼滅)을 각각 100mg/kg(RGL) 및 200mg/kg(RGH)씩 인체의 간유(肝兪)($BL_{18}$)에 상응하는 혈위에 1일 1회 10주간 좌우 혈을 번갈아가며 약침 시술하였다. 양성대조군은 metformin 300mg/kg(MET), glipizide 15mg/kg(GPZ) 및 pioglitazone 30mg/kg(PIO)을 각각 1일 1회 10주간 경구투여 하였다. 체중과 혈당은 매주 측정하였다. 실험 10주 후에는 혈액채취로 혈중 glucose, 당화혈색소(HbAlc), insulin, 중성지방(TG), adiponectin, leptin, non-esterified fatty acid(NEFA)를 측정 하였고, 간 조직을 채취하여 조직학적 검사 및 gene expression 분석을 시행하였다. 결과 : 홍삼약침(藥鍼)(RGL, RGH)은 10주 동안 C57BL/KsJ db/db mice의 체중을 증가시키는 부작용은 나타나지 않았다. 홍삼약침(藥鍼)군(RGL, RGH)의 사료섭취량은 대조군과 비슷하였으나 음수량은 증가하였다. 홍삼약침(藥鍼)(RGL, RGH)은 대조군에 비하여 각각 19.8% 및 18.3% 혈당을 낮추었고, 홍삼약침(藥鍼)(RGL)은 insulin resistance를 27.7% 감소시켰으며, 경구내당능 검사의 혈중 glucose에서는 대조군에 비해 홍삼약침(藥鍼)군(RGL, RGH)과 양성대조군(MET, GPZ, PIO)에서 각각 19.8%, 18.3%, 67.7%, 52.3% 및 56.9% 감소시켰다. 당화혈색소(HbAlc)는 홍삼약침(藥鍼)(RGL, RGH), MET, GPZ 및 PIO군에서 대조군에 비하여 각각 11.0%, 6.4%, 18.9%, 16.1% 및 27.9% 감소시켰으며, 혈중 glucose감소와 유사한 경향을 나타내었다. 홍삼약침(藥鍼)(RGL)은 대조군에 비해 TG와 NEFA를 각각 18.8% 및 16.8% 감소시켰고, adiponectin과 leptin을 각각 20.6% 및 12.1% 증가시켰다. 홍삼약침(藥鍼)(RGL, RGH)은 중성지방의 침착으로 인한 간의 질량비 증가를 억제하지 못하였으나, 지방구를 감소시겼음을 관찰할 수 있었다. Microarray 분석에서는 홍삼약침(藥鍼)(RGL, RGH)이 간에서 glycolysis, gluconeogenesis 및 fatty acid beta-oxidation과 관련된 유전자 발현에 영향을 미치는 것으로 나타나 양성대조군 metformin과 유사한 기전을 나타내었다. 요약 : 홍삼약침(藥鍼)은 T2DM동물모델(C57BL/KsJ db/db mice)에서 항당뇨 및 지질대사 개선활성이 있었다. 홍삼약침(藥鍼)은 C57BL/KsJ db/db mice의 간조직에서 lipogenesis억제 및 fatty acid beta-oxidation활성을 통해 혈당 이용을 높이고, insulin sensitivity를 향상시켰다. 또한 유전자 발현분석을 통해 그 기전이 metformin과 유사함을 확인할 수 있었으므로 향후 홍삼약침(藥鍼)의 새로운 약침 기술 개발 근거가 될 수 있을 것으로 사료된다.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.3
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• pp.157-165
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• 2006

The change of external/internal factors of the cell rquires specific biological functions to maintain life. Such functions encourage particular genes to jnteract/regulate each other in multiple ways. Accordingly, we applied a linear decomposition model IFSA, which derives hidden variables, called the 'expression mode' that corresponds to the functions. To interpret gene interaction/regulation, we used a cross-correlation method given an expression mode. Linear decomposition models such as principal component analysis (PCA) and independent component analysis (ICA) were shown to be useful in analyzing high dimensional DNA microarray data, compared to clustering methods. These methods assume that gene expression is controlled by a linear combination of uncorrelated/indepdendent latent variables. However these methods have some difficulty in grouping similar patterns which are slightly time-delayed or asymmetric since only exactly matched Patterns are considered. In order to overcome this, we employ the (IFSA) method of [1] to locate phase- and shut-invariant features. Membership scoring functions play an important role to classify genes since linear decomposition models basically aim at data reduction not but at grouping data. We address a new function essential to the IFSA method. In this paper we stress that IFSA is useful in grouping functionally-related genes in the presence of time-shift and expression phase variance. Ultimately, we propose a new approach to investigate the multiple interaction information of genes.

• International Journal of Oral Biology
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• v.32 no.1
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• pp.35-43
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• 2007

Tooth loss in elderly is mainly caused by alveolar bone loss via severe periodontitis. Although the severity of periodontitis is known to be affected by age, the aging process or the genetic changes during the aging of periodontal tissue cells are not well characterized. In this study, we investigated the effect of in vitro aging on the change of gene expression pattern in periodontal fibroblasts. Gingival fibroblasts (GF) and periodontal ligament fibroblasts (PDL) were obtained from two young patients and replicative senescence was induced by sequential subcultivation. When more than 90% cells were positively stained with senescence-associated ${\beta},-galactosidase$, those cells were regarded as aged cells. In aged GF and PDL, the level of phosphorylated retinoblastoma (RB) and $p16^{INK4A}$ protein was significantly decreased and increased, respectively. However, the protein level of p53 and p21, well known senescence-inducing genes, did not increase in aged GF and PDL. Although $p27^{Kip1}$ and $p15^{INK4B}$, another cyclin-dependent kinase inhibitors, were reported to be involved in replicative senescence of human cells, they were decreased in aged GF and PDL. Because senescent cells showed flattened and enlarged cell shape and are known to have increased focal adhesion, we examined the protein level of several integrins. Aged GF and PDL showed increased protein level of integrin ${\alpha}2$, ${\alpha}v$, and ${\beta}1$. When the gene expression profiles of actively proliferating young cells and aged cells were compared by cDNA microarray of 3,063 genes and were confirmed by reverse transcription-polymerase chain reaction, 7 genes and 15 genes were significantly and commonly increased and decreased, respectively, in aged GF and PDL. Among them, included are the genes that were known to be involved in the regulation of cell cycle, gene transcription, or integrin signaling. The change of gene expression pattern in GF and PDL was minimally similar to that of oral keratinocyte. These results suggest that $p16^{INK4A}/RB$ might be involved in replicative senescence of periodontal fibroblasts and the change of gene expression profile during aging process is cell type specific.

• Childhood Kidney Diseases
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• v.15 no.1
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• pp.38-48
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• 2011

Purpose: Focal segmental glomerulosclerosis (FSGS) is the most common glomerulopathy causing pediatric renal failure. Since specific treatment targeting the etiology and pathophysiology of primary FSGS is yet elusive, the authors explored the pathophysiology of FSGS by transcriptome analysis of the disease using an animal model. Methods: FGS/kist strain, a mouse model of primary FSGS, and RFM/kist strain, as control and the parent strain of FGS/kist, were used. Kidney tissues were harvested and isolated renal cortex was used to extract mRNA, which was run on AB 1700 mouse microarray chip after reverse transcription to get the transcriptome profile. Results: Sixty two genes were differentially expressed in FGS/kist kidney tissue compared to the control. Those genes were related to cell cycle/cell death, immune reaction, and lipid metabolism/vasculopathy, and the key molecules of their networks were TNF, IL-6/4, IFN${\gamma}$, TP53, and PPAR${\gamma}$. Conclusion: This study confirmed that renal cell death, immune system activation with subsequent fibrosis, and lipid metabolism-related early vasculopathy were involved in the pathophysiology of FSGS. In addition, the relevance of methodology used in this study, namely transcriptome profiling, and Korean animal model of FGS/kist was validated. Further study would reveal novel pathophysiology of FSGS for new therapeutic targets.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.15 no.11
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• pp.6774-6781
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• 2014

This study examined the efficacy and the mechanism of action of biological response modifiers, ginsenosides Rb1 and Rg1 isolated from Panax ginseng C.A. Meyer on human keratinocytes HaCaT cell lines. A non-significant cytotoxic response was obtained in the HaCaT cell lines on treatment with various concentrations of ginsenosides Rb1 and Rg1 for different time durations. Furthermore, the global changes in the mRNA profile of HaCaT cells were investigated using DNA microarrays after stimulation with the ginsenosides Rb1 and Rg1. Ginsenosides Rb1 and Rg1 strongly increased FGF2 in HaCaT cells, and were found to be a candidate gene for antioxidant activity and elasticity. Other key candidate genes for antioxidant activity, such as FANCD2, LEPR, and FAS, also show enhanced regulation in HaCaT cells treated with ginsenoside Rb1. This study will be useful for understanding the regulatory genes involved in skin elasticity and signal transduction pathway stimulated by the ginsenoside Rb1. This paper currently focuses on the key factors regulating the interaction of anti-aging principles and skin elasticity.

• Journal of Microbiology and Biotechnology
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• v.30 no.10
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• pp.1480-1487
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• 2020

Our previous report determined that miR-144 is a key regulator of intestinal epithelial permeability in irritable bowel syndrome with diarrhea (IBS-D) rats. Recent evidence has shown that lactobacilli play an important role in the relief of IBS-D symptoms. However, few studies have addressed the mechanisms by which microRNAs and lactobacilli exert their beneficial effects on intestinal epithelial permeability. Hence, to elucidate whether miRNAs and lactobacilli play roles in intestinal epithelial barrier regulation, we compared miRNA expression levels in intestinal epithelial cells (IECs) under Lactobacillus casei (L. casei LC01) treatment. IECs and L. casei LC01 were co-cultured and then subjected to microRNA microarray assay. qRT-PCR, western blot and ELISA were used to detect the expression of occludin (OCLN) and zonula occludens 1 (ZO1/TJP1). The interaction between miRNAs and L. casei LC01 acting in IECs was investigated through transfection of RNA oligoribonucleotides and pcDNA 3.1 plasmid. The results are as follows: 1) L. casei LC01 decreased the expression of miR-144 and FD4 and promoted OCLN and ZO1 expression in IECs; 2) L. casei LC01 enhanced the barrier function of IECs via downregulation of miR-144 and upregulation of OCLN and ZO1; 3) Under L. casei LC01 treatment, OCLN and ZO1 overexpression could partially eliminate the promoting effect of miR-144 on intestinal permeability in IECs. Our results demonstrate that L. casei LC01 regulates intestinal permeability of IECs through miR-144 targeting of OCLN and ZO1. L. casei LC01 can be a possible therapeutic target for managing dysfunction of the intestinal epithelial barrier.

• The Journal of Pediatrics of Korean Medicine
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• v.16 no.1
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• pp.39-74
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• 2002

Recently, increased attention has been paid to the growth of the height of children and adolescents. To accelerate growth, velvet antlers are typically used in Oriental medicine. The present study investigated the effects of velvet antlers of velvet antlers on bone growth using the cell line of Human Osteosarcoma (Hos), derived from the bone-generating cells essential to bone growth. In order to give certain stress to this Hos, the medium contained 1% FBS was used for culturing for Hos cell instead of 10% in control. In this condition of which the proliferation had been significantly decreased, the ethanol extract of upper part of velvet antlers was added, As a result, the cells proliferation rate was significantly increased. Using Oligonucleotide DNA microarray, comparison and analyses were done to see what kind of specific genes would be differentially expressed. The result showed that as opposed to the control group, the stressed group indicated a decrease in the expressions of 6 kinds of genes such as, Id1, retinoid X receptor(RXRB) and 14-3-3 epsilon, etc. The velvet antler treated group, as opposed to the control group, showed a decreased in the expressions of 8 kinds of genes such as Id1, etc. and an increase in the expressions of 24 kinds of genes. The number of genes that showed differences in the velvet antler treated group compared with the stressed group was 7 the expression of 1 kind of gene was decreased, and the expressions of 6 kinds of genes were increased. Considering the mechanism by which velvet antlers affected the growth of osteoblast through reviewing the functions of these genes, the following results were attained. The constraint in the proliferation of Hos cells resulting from the medium contained 1% FBS seems to be caused by three important factors: 1) the decrease of the expression of 14-3-3 epsilon involved in the signal transduction and metabolism of growth, 2) the decrease of the expression of Id1 gene involved in the metabolism of bone formation, and 3) the decreased of expression of RXRB gene involved in the metabolism of retinoci acid. It is suggested that the improvement of the cell proliferating effects by velvet antler treatment, in stressed condition si mediated by increment of 6 genes particularly 14-3-3 epsilon, RXRB, and IGF2, with are the crucial factors for the cell growth and differentiation, metabolism of retinoic acid and osteoblast proliferation, respectively.