• Toxicological Research
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• v.25 no.2
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• pp.85-92
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• 2009

4,4'-Methylenedianiline (MDA) is an aromatic amine that is widely used in the industrial synthetic process. Genotoxic MDA forms DNA adducts in the liver and is known to induce liver damage in human and rats. To elucidate the molecular mechanisms associated with MDA-induced hepatotoxicity, we have identified genes differentially expressed by microarray approach. BALB/c male mice were treated once daily with MDA (20 mg/kg) up to 7 days via intraperitoneal injection (i.p.) and hepatic damages were revealed by histopathological observation and elevation of serum marker enzymes such as AST, ALT, ALP, cholesterol, DBIL, and TBIL. Microarray analysis showed that 952 genes were differentially expressed in the liver of MDA-treated mice and their biological functions and canonical pathways were further analyzed using Ingenuity Pathways Analysis (IPA). Toxicological functional analysis showed that genes related to hepatotoxicity such hyperplasia/hyperproliferation (Timp1), necrosis/cell death (Cd14, Mt1f, Timp1, and Pmaip1), hemorrhaging (Mt1f), cholestasis (Akr1c3, Hpx, and Slc10a2), and inflammation (Cd14 and Hpx) were differentially expressed in MDA-treated group. This gene expression profiling should be useful for elucidating the genetic events associated with aromatic amine-induced hepatotoxicity and for discovering the potential biomarkers for hepatotoxicity.

• Molecular & Cellular Toxicology
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• v.3 no.4
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• pp.222-230
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• 2007

Some drugs may be limited in their clinical application due to their propensity towards their adverse effects. Toxicogenomic technology represents a useful approach for evaluating the toxic properties of new drug candidates early in the drug discovery process. Nitrofurantoin (NF) is clinical chemotherapeutic agent and antimicrobial and used to treatment of urinary tract infections. However, NF has been shown to result in pulmonary toxic effects. In this research, we revealed the changing expression gene profiles in BEAS-2B, human bronchial epithelial cell line, exposed to NF by using human oligonucleotide chip. Through the clustering analysis of gene expression profiles, we identified 136 up-regulated genes and 379 down-regulated genes changed by more than 2-fold by NF. This study identifies several interesting targets and functions in relation to NF-induced toxicity through a gene ontology analysis method including biological process, cellular components, molecular function and KEGG pathway.

• The Korea Genome Conference
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• 2005.09a
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• pp.65-65
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• 2005

• Journal of Ginseng Research
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• v.40 no.1
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• pp.1-8
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• 2016

Background: Korean Red Ginseng (KRG) is a herbal medicine used in Asian countries and is very popular for its beneficial biological properties. Diabetes mellitus (DM) and its complications are rapidly becoming a global public health concern. The literature on transcriptional changes induced by KRG in rat models of diabetic retinopathy is limited. Considering these facts, we designed this study to determine whether retinopathy-associated genes are altered in retinas of rats with DM and whether the induced changes are reversed by KRG. Methods: Male Sprague-Dawley rats were intravenously injected with streptozotocin (50 mg/kg body weight) to induce DM, following which, KRG powder (200 mg/kg body weight) was orally administered to the KRG-treated DM rat group for 10 wks. The rats were then sacrificed, and their retinas were harvested for total RNA extraction. Microarray gene expression profiling was performed on the extracted RNA samples. Results: From among > 31,000 genes investigated, the expression of 268 genes was observed to be upregulated and that of 58 genes was downregulated, with twofold altered expression levels in the DM group compared with those in the control group. Moreover, 39 genes were upregulated more than twofold and 84 genes were downregulated in the KRG-treated group compared to the DM group. The expression of the genes was significantly reversed by KRG treatment; some of these genes were analyzed further to verify the results of the microarray experiments. Conclusion: Taken together, our data suggest that reversed changes in the gene expression may mediate alleviating activities of KRG in rats with diabetic retinopathy.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.45-52
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• 2000

Genomic approach produces massive amount of data within a short time period, New high-throughput automatic sequencers can generate over a million nucleotide sequence information overnight. A typical DNA chip experiment produces tens of thousands expression information, not to mention the tens of megabyte image files, These data must be handled automatically by computer and stored in electronic database, Thus there is a need for systematic approach of data collection, processing, and analysis. DNA sequence information is translated into amino acid sequence and is analyzed for key motif related to its biological and/or biochemical function. Functional genomics will play a significant role in identifying novel drug targets and diagnostic markers for serious diseases. As an enabling technology for functional genomics, bioinformatics is in great need worldwide, In Korea, a new functional genomics project has been recently launched and it focuses on identi☞ing genes associated with cancers prevalent in Korea, namely gastric and hepatic cancers, This involves gene discovery by high throughput sequencing of cancer cDNA libraries, gene expression profiling by DNA microarray and proteomics, and SNP profiling in Korea patient population, Our bioinformatics team will support all these activities by collecting, processing and analyzing these data.

• BMB Reports
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• v.48 no.7
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• pp.388-394
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• 2015

The brain is an organ that consists of various cell types. As our knowledge of the structure and function of the brain progresses, cell type-specific research is gaining importance. Together with advances in sequencing technology and bioinformatics, cell type-specific transcriptome studies are providing important insights into brain cell function. In this review, we discuss 3 different cell type-specific transcriptome analyses i.e., Laser Capture Microdissection (LCM), Translating Ribosome Affinity Purification (TRAP)/RiboTag, and single cell RNA-Seq, that are widely used in the field of neuroscience. [BMB Reports 2015; 48(7): 388-394]

• Journal of Gastric Cancer
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• v.17 no.1
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• pp.43-51
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• 2017

Purpose: This study aimed to analyze G3BP1 and VEZT expression profiles in patients with gastric cancer, and examine the possible relationship between the expressions of each gene and clinicopathological factors. Materials and Methods: Expression of these genes in formalin-fixed paraffin embedded (FFPE) tissues, collected from 40 patients with gastric cancer and 40 healthy controls, was analyzed. Differences in gene expression among patient and normal samples were identified using the GraphPad Prism 5 software. For the analysis of real-time polymerase chain reaction products, GelQuantNET software was used. Results: Our findings demonstrated that both VEZT and G3BP1 mRNA expression levels were downregulated in gastric cancer samples compared with those in the normal controls. No significant relationship was found between the expression of these genes and gender (P-value, 0.4835 vs. 0.6350), but there were significant changes associated with age (P-value, 0.0004 vs. 0.0001) and stage of disease (P-value, 0.0019 vs. 0.0001). In addition, there was a direct relationship between VEZT gene expression and metastasis (P-value, 0.0462), in contrast to G3BP1 that did not demonstrate any significant correlation (P-value, 0.1833). Conclusions: The results suggest that expression profiling of VEZT and G3BP1 can be used for diagnosis of gastric cancer, and specifically, VEZT gene could be considered as a biomarker for the detection of gastric cancer progression.

• The Korea Genome Conference
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• 2006.09a
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• pp.45-45
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• 2006

• The Korea Genome Conference
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• 2003.09a
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• pp.38.1-38.1
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• 2003

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.02a
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• pp.19-19
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• 2003

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