• Journal of Gastric Cancer
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• v.5 no.3 s.19
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• pp.200-205
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• 2005

Purpose: KLF4, a member of the KLF family, is a zinc finger tumor suppressor protein that is critical for gastric epithelial homeostasis. Our aim was to determine whether the altered expression of KLF4 might be associated with gastric cancer development and, if so, to determine to which pathologic parameter it is linked. Materials and Methods: For the construction of the gastric cancer tissue microarray, 84 paraffin-embedded tissues containing gastric cancer areas were cored 3 times and transferred to the recipient master block. The expression pattern of KLF4 was examined on tissue microarray slides by using immunohistochemistry and was compared with pathologic parameters, including histologic type, depth of invasion, lymph node metastasis, and peritoneal dissemination. Results: The KLF4 protein was expressed in cytoplasm and nucleus of superficial and foveolar epithelial cells in the normal gastric mucosa. We found markedly reduced or loss of KLF4 expression in 43 (51.2%) of the 84 gastric cancer tissues. There was no significant correlation between KLF4 expression and pathologic parameters, including histologic type, depth of invasion, lymph node metastasis and peritoneal dissemination. Conclusion: Our findings suggest that altered expression of KLF4 may contribute to abnormal regulation of gastrointestinal epithelial cell growth and differentiation and to the development of Korean gastric cancer, as an early event.

• Journal of Oriental Neuropsychiatry
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• v.26 no.1
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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.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.102-111
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• 2016

The goal of this study was to characterize the BrDSR (Drought Stress Resistance in B. rapa) gene and to identify the expression network of drought-inducible genes in Chinese cabbage under drought stress. Agrobacterium-mediated transformation was conducted using a B. rapa inbred line ('CT001') and the pSL100 vector containing the BrDSR full length CDS (438 bp open reading frame). Four transgenic plants were selected by PCR and the expression level of BrDSR was approximately 1.9-3.4-fold greater than that in the wild-type control under drought stress. Phenotypic characteristics showed that BrDSR over-expressing plants were resistant to drought stress and showed normal growth habit. To construct a co-expression network of drought-responsive genes, B. rapa 135K cDNA microarray data was analyzed to identify genes associated with BrDSR. BrDSR was directly linked to DARK INDUCIBLE 2 (DIN2, AT3G60140) and AUTOPHAGY 8H (ATG8H, AT3G06420) previously reported to be leaf senescence and autophagy-related genes in plants. Taken together, the results of this study indicated that BrDSR plays a significant role in enhancement of tolerance to drought conditions.

• Journal of Plant Biotechnology
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• v.35 no.2
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• pp.133-140
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• 2008

The modification of DNA and histone plays an important role for gene expression in plant development. The objective of this research is to observe the effects of methylation on the gene expression during dedifferentiation from rice mature seeds to callus and differentiation from callus to shoots. The embryogenic callus with ability to shoot regeneration was not induced on the N6A medium supplemented with 5-azacytidine and abnormal callus with brown color was formed. When the normal rice callus was placed on the regeneration MSRA medium supplemented with 5-azacytidine, the shoot regeneration was inhibited. The results showed that 5-azacytidine, DNA demethylating agent, had negative effects on normal embryogenic callus formation and shoot regeneration. This suggested that DNA methylation of some genes was required for normal cell dedifferentiation and differentiation in tissue culture. The microarray and $GeneFishig^{TM}$ DEG screening were used to observe the gene transcript profile in callus induction and regeneration on N6A (N6 medium + 5-azaC) and MSRA (MS regeneration medium + 5-azaC). Subsets of genes were up-regulated or down-regulated in response to 5-azaC treatments. The genes related with epigenetic regulation, electron transport, nucleic acid metabolism and response to stress were up and down regulated. The different expression of some genes (germin like protein etc.) during callus induction and shoot regeneration was confirmed using RT-PCR and northern blot analysis.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.15 no.3
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• pp.127-137
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• 2015

Purpose: The main aim of this study was to compare and analyze expression profiles of microRNAs (miRNAs) to establish miRNA signature of Fabry nephropathy related epithelial mesenchymal transition (EMT). Methods: Expression profiles of miRNAs in kidney tissue samples and cell lines from normal and Fabry disease mouse model were examined by miRNA expression microarray analysis followed by quantitative real-time polymerase chain reaction analysis (qRT-PCR). Results: In the miRNA expression microarray analysis of Fabry mouse kidney tissues compared to wild type mouse, 5 and 3 miRNAs among 1,247 miRNAs examined were up- and down-regulated, respectively. Among them, miR-149-5p was down-regulated about 2-fold in Fabry kidney samples. The down-regulations of miR-149-5p were observed in kidney tissues of under 35 week-old-Fabry mice. However, this down-regulation was not observed in kidney tissues of 42 week-old Fabry mice. In SV40 MES 13 cells, mouse mesangial cells, treated with globotriaosylsphingosine (lyso-Gb3), miR-149-5p was also downregulated. The down-regulation of miR-149-5p induced up-regulation of its target genes related to EMT. Conclusion: The miRNA expression array and qRT-PCR results show that miR-149-5p expression was decreased in kidney tissues of Fabry mice compared to wild type mice under 35 weeks of age. Along with the observation of miR-149-5p expression in Fabry disease cell models, these results indicate that the down-regulated miR-149-5p were related to the biological response of mesangial cells to lyso-Gb3 and also have influence to the transcriptional up-regulation of its target genes. These results suggest miR-149-5p might play important roles in the Fabry nephropathy.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.9
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• pp.4013-4018
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• 2014

Because of its importance in tumor invasion and metastasis, the epithelial-mesenchymal transition (EMT) has become a research focus in the field of cancer. Recently, evidence has been presented that FoxO4 might be involved in EMT. Our study aimed to detect the expression of FoxO4, E-cadherin and vimentin in non-small cell lung cancers (NSCLCs). We also investigated clinical features and their correlations with the markers. In our study, FoxO4, E-cadherin and vimentin were assessed by immunohistochemistry in a tissue microarray (TMA) containing 150 cases of NSCLC. In addition, the expression level of FoxO4 protein was determined by Western blotting. The percentages of FoxO4, E-cadherin and vimentin positive expression in NSCLCs were 42.7%, 38.7% and 55.3%, respectively. Immunoreactivity of FoxO4 was low in NSCLC when compared with paired normal lung tissues. There were significant correlations between FoxO4 and TNM stage (P<0.001), histological differentiation (P=0.004) and lymph node metastasis (P<0.001), but no significant links with age (P=0.323), gender (P=0.410), tumor size (P=0.084), smoking status (P=0.721) and histological type (P=0.281). Our study showed that low expression of FoxO4 correlated with decreased expression of E-cadherin and elevated expression of vimentin. Cox regression analysis indicated FoxO4 to be an independent prognostic factor in NSCLC (P=0.046). These data suggested that FoxO4 might inhibit the process of EMT in NSCLC, and might therefore be a target for therapy.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5799-5804
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• 2012

Family with sequence similarity 189, member B (FAM189B), alias COTE1, a putative oncogene selected by microarray, for the first time was here found to be significantly up-regulated in hepatocellular carcinoma (HCC) specimens and HCC cell lines. mRNA expression of COTE1 in HCC samples and cell lines was detected by reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR, while protein expression of COTE1 in HCC tissues was assessed by immunohistochemistry. In addition, invasion of HCC cells was observed after overexpressing or silencing COTE1. In the total of 48 paired HCC specimens, compared with the adjacent non-cancer tissues, the expression of COTE1 was up-regulated in 31 (p<0.01). In HCC cell lines, COTE1 expression was significantly higher than in normal human adult liver (p<0.01). Overexpression of COTE1 enhanced HCC-derived LM6 and MHCC-L cellular invasion in vitro. In contrast, COTE1 knockdown via RNAi markedly suppressed these phenotypes, as documented in LM3 and MHCC-H HCC cells. Mechanistic analyses indicated that COTE1 could physically associate with WW domain oxidoreductase (WWOX), a tumor suppressor. COTE1 may be closely correlated with invasion of hepatocellular carcinoma (HCC) cells and thus may serve as an effective target for gene therapy.

• Clinical and Experimental Pediatrics
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• v.60 no.9
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• pp.282-289
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• 2017

Purpose: Recent advancements in molecular techniques have greatly contributed to the discovery of genetic causes of unexplained developmental delay. Here, we describe the results of array comparative genomic hybridization (CGH) and the clinical features of 27 patients with global developmental delay. Methods: We included 27 children who fulfilled the following criteria: Korean children under 6 years with global developmental delay; children who had at least one or more physical or neurological problem other than global developmental delay; and patients in whom both array CGH and G-banded karyotyping tests were performed. Results: Fifteen male and 12 female patients with a mean age of $29.3{\pm}17.6months$ were included. The most common physical and neurological abnormalities were facial dysmorphism (n=16), epilepsy (n=7), and hypotonia (n=7). Pathogenic copy number variation results were observed in 4 patients (14.8%): 18.73 Mb dup(2)(p24.2p25.3) and 1.62 Mb del(20p13) (patient 1); 22.31 Mb dup(2) (p22.3p25.1) and 4.01 Mb dup(2)(p21p22.1) (patient 2); 12.08 Mb del(4)(q22.1q24) (patient 3); and 1.19 Mb del(1)(q21.1) (patient 4). One patient (3.7%) displayed a variant of uncertain significance. Four patients (14.8%) displayed discordance between G-banded karyotyping and array CGH results. Among patients with normal array CGH results, 4 (16%) revealed brain anomalies such as schizencephaly and hydranencephaly. One patient was diagnosed with Rett syndrome and one with $M{\ddot{o}}bius$ syndrome. Conclusion: As chromosomal microarray can elucidate the cause of previously unexplained developmental delay, it should be considered as a first-tier cytogenetic diagnostic test for children with unexplained developmental delay.

• Molecules and Cells
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• v.41 no.4
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• pp.351-361
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• 2018

Sucrose is a crucial compound for the growth and development of plants, and the regulation of multiple genes depends on the amount of soluble sugars present. Sucrose acts as a signaling molecule that regulates a proton-sucrose symporter, with its sensor being the sucrose transporter. Flavonoid and anthocyanin biosynthesis are regulated by sucrose, and sucrose signaling can affect flavonoid and anthocyanin accumulation. In the present study, we found a Myb transcription factor affecting accumulation of anthocyanin. AtMyb56 showed an increase in its expression in response to sucrose treatment. Under normal conditions, anthocyanin accumulation was similar between Col-0 (wild type) and atmyb56 mutant seedlings; however, under sucrose treatment, the level of anthocyanin accumulation was lower in the atmyb56 mutant plants than in Col-0 plants. Preliminary microarray analysis led to the investigation of the expression of one candidate gene, AtGPT2, in the atmyb56 mutant. The phosphate translocator, which is a plastidial phosphate antiporter family, catalyzes the import of glucose-6-phosphate (G-6-P) into the chloroplast. AtGPT2 gene expression was altered in atmyb56 seedlings in a sucrose-dependent manner in response to circadian cycle. Furthermore, the lack of AtMyb56 resulted in altered accumulation of maltose in a sucrose-dependent manner. Therefore, the sucrose responsive AtMyb56 regulates AtGPT2 gene expression in a sucrose-dependent manner to modulate maltose and anthocyanin accumulations in response to the circadian cycle.

• Molecular & Cellular Toxicology
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• v.1 no.1
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• pp.62-71
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• 2005

For toxicity model in the kidney, renal cell carcinoma (RCC) is one of the most important model to assess the structural and functional alterations. Most RCCs are sporadic, and environmental agents are suspected to play a role in the etiology of the disease. In this study, we discovered novel evidence for previously unknown gene expression patterns related to progression according to cancer stage in RCC. Four clear cell RCC tissue samples along with five corresponding patient-matched normal kidney tissue samples were obtained from patients undergoing partial or radical nephrectomy. To examine the difference of gene expression profile in clear cell RCC, radioactive cDNA microarrays were used to evaluate changes in the expression of 1,152 genes in a total. Using $^{33}P-labeled$ probes, this method provided highly sensitive gene expression profiles including drug metabolism, and cellular signaling. 29 genes were identified with expression levels that differed by more than 2.0 value of z-ratio, compared with that in control. Whereas expression of 38 genes were decreased by less than-2.0 value of z-ratio. In conclusion, this study has identified 67 gene expression alterations in clear-cell type of RCC. Most notably, genes involved in cell growth were up-regulated in stage I more than stage III whereas genes involved in signal transduction were down-regulated in which both stage I and stage III. The identified alteraions of gene expression will likely give in sight in to clear cell RCC and tumor progression.