• Journal of the Korea Society of Computer and Information
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• v.21 no.3
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• pp.65-71
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• 2016

To reduce the expenses for development a novel drug, systems biology has been studied actively. Target prediction, a part of systems biology, contributes to finding a new purpose for FDA(Food and Drug Administration) approved drugs and development novel drugs. In this paper, we propose a classification model for predicting novel target genes based on relation between target genes and disease related genes. After collecting known target genes from TTD(Therapeutic Target Database) and disease related genes from OMIM(Online Mendelian Inheritance in Man), we analyzed the effect of target genes on disease related genes based on PPI(Protein-Protein Interactions) network. We focused on the distinguishing characteristics between known target genes and random target genes, and used the characteristics as features for building a classifier. Because our model is constructed using information about only a disease and its known targets, the model can be applied to unusual diseases without similar drugs and diseases, while existing models for finding new drug-disease associations are based on drug-drug similarity and disease-disease similarity. We validated accuracy of the model using LOOCV of ten times and the AUCs were 0.74 on Alzheimer's disease and 0.71 on Breast cancer.

• Molecules and Cells
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• v.43 no.11
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• pp.935-944
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• 2020

Aryl hydrocarbon receptor nuclear translocator (ARNT) plays an essential role in maintaining cellular homeostasis in response to environmental stress. Under conditions of hypoxia or xenobiotic exposure, ARNT regulates the subset of genes involved in adaptive responses, by forming heterodimers with hypoxia-inducible transcription factors (HIF1α and HIF2α) or aryl hydrocarbon receptor (AhR). Here, we have shown that ARNT interacts with DDB1 and CUL4-associated factor 15 (DCAF15), and the aryl sulfonamides, indisulam and E7820, induce its proteasomal degradation through Cullin-RING finger ligase 4 containing DCAF15 (CRL4^DCAF15) E3 ligase. Moreover, the two known neo-substrates of aryl sulfonamide, RNA-binding motif protein 39 (RBM39) and RNA-binding motif protein 23 (RBM23), are not required for ARNT degradation. In line with this finding, aryl sulfonamides inhibited the transcriptional activities of HIFs and AhR associated with ARNT. Our results collectively support novel regulatory roles of aryl sulfonamides in both hypoxic and xenobiotic responses.

• Molecules and Cells
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• v.42 no.10
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• pp.729-738
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• 2019

Autophagy is an important process for protein recycling. Oligomerization of p62/SQSTM1 is an essential step in this process and is achieved in two steps. Phox and Bem1p (PB1) domains can oligomerize through both basic and acidic surfaces in each molecule. The ZZ-type zinc finger (ZZ) domain binds to target proteins and promotes higher-oligomerization of p62. This mechanism is an important step in routing target proteins to the autophagosome. Here, we determined the crystal structure of the PB1 homo-dimer and modeled the p62 PB1 oligomers. These oligomer models were represented by a cylindrical helix and were compared with the previously determined electron microscopic map of a PB1 oligomer. To accurately compare, we mathematically calculated the lead length and radius of the helical oligomers. Our PB1 oligomer model fits the electron microscopy map and is both bendable and stretchable as a flexible helical filament.

• BMB Reports
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• v.53 no.7
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• pp.373-378
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• 2020

Phosphorylation of the signaling component by protein kinase often leads to a kinase cascade or feedback loop. 3-Phosphoinositide-dependent kinase 1 (PDK1) signaling pathway diverges into various kinases including Akt and p70 S6 kinase (p70S6k). However, the PDK1 feedback mechanism remains elusive. Here, we demonstrated that UNC-51-like kinase (ULK1), an autophagy initiator kinase downstream of mechanistic target of rapamycin (mTOR), directly phosphorylated PDK1 on serine 389 at the linker region. Furthermore, our data showed that this phosphorylation affected the kinase activity of PDK1 toward downstream substrates. These results suggest a possible negative feedback loop between PDK1 and ULK1.

• Molecules and Cells
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• v.44 no.7
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• pp.458-467
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• 2021

GPR43 (also known as FFAR2 or FFA2) is a G-protein-coupled receptor primarily expressed in immune cells, enteroendocrine cells and adipocytes that recognizes short-chain fatty acids, such as acetate, propionate, and butyrate, likely to be implicated in innate immunity and host energy homeostasis. Activated GPR43 suppresses the cAMP level and induces Ca²⁺ flux via coupling to Gα_i and Gα_q families, respectively. Additionally, GPR43 is reported to facilitate phosphorylation of ERK through G-protein-dependent pathways and interacts with β-arrestin 2 to inhibit NF-κB signaling. However, other G-protein-dependent and independent signaling pathways involving GPR43 remain to be established. Here, we have demonstrated that GPR43 augments Rho GTPase signaling. Acetate and a synthetic agonist effectively activated RhoA and stabilized YAP/TAZ transcriptional coactivators through interactions of GPR43 with Gα_q/11 and Gα_12/13. Acetate-induced nuclear accumulation of YAP was blocked by a GPR43-specific inverse agonist. The target genes induced by YAP/TAZ were further regulated by GPR43. Moreover, in THP-1-derived M1-like macrophage cells, the Rho-YAP/TAZ pathway was activated by acetate and a synthetic agonist. Our collective findings suggest that GPR43 acts as a mediator of the Rho-YAP/TAZ pathway.

• BMB Reports
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• v.49 no.10
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• pp.560-565
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• 2016

Granzyme A (GzmA) was first identified as a cytotoxic T lymphocyte protease protein with limited tissue expression. A number of cellular proteins are known to be cleaved by GzmA, and its function is to induce apoptosis. Histones H1, H2B, and H3 were identified as GzmA substrates during apoptotic cell death. Here, we demonstrated that histone H4 was cleaved by GzmA during staurosporine-induced cell death; however, in the presence of caspase inhibitors, staurosporine-treated Raji cells underwent necroptosis instead of apoptosis. Furthermore, histone H4 cleavage was blocked by the GzmA inhibitor nafamostat mesylate and by GzmA knockdown using siRNA. These results suggest that histone H4 is a novel substrate for GzmA in staurosporine-induced cells.

• Herbal Formula Science
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• v.28 no.3
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• pp.243-254
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• 2020

Objectives : Network pharmacology analysis is commonly used to investigate the synergies and potential mechanisms of multiple compounds by analyzing complex, multi-layered networks. We used TCMSP and BATMAN-TCM databases to compare results of network pharmacological analysis between White Ginseng(WG) and Red Ginseng(RG). Methods : WG and RG were compared with components and their target molecules using TCMSP database, and compound-target-pathway/disease networks were compared using BATMAN-TCM database. Results : Through TCMSP, 104 kinds of target molecules were derived from WG and 38 kinds were derived from RG. Using the BATMAN-TCM database, target pathways and diseases were screened, and more target pathways and diseases were screened compared to RG due to the high composition of WG ingredients. Analysis of component-target-pathway/disease network using network analysis tools provided by BATMAN-TCM showed that WG formed more networks than RG. Conclusions : Network pharmacology analysis can be effectively performed using various databases used in system biology research, and although the materials that have been reported in the past can be used efficiently for research on diseases related to targets, the results are unreliable if prior studies are focused on limited or narrow research areas.

• The Korean Journal of Physiology and Pharmacology
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• v.27 no.5
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• pp.457-470
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• 2023

The aim of this study was to investigate the role of kinesin superfamily member 15 (KIF15) in nasopharyngeal carcinogenesis (NPC) and explore its underlying mechanisms. We employed various assays, including the CCK-8 assay, flow cytometry, the Transwell and scratch assay, Western blotting, and nude mice transplantation tumor, to investigate the impact of KIF15 on NPC. Our findings demonstrate that KIF15 plays a critical role in the proliferation, apoptosis, migration, and invasion of NPC cells. Furthermore, we discovered that silencing KIF15 inhibits cell proliferation, migration, and invasion while promoting apoptosis, and that KIF15's effect on NPC cell growth is mediated through the PI3K/AKT and P53 signaling pathways. Additionally, we showed that KIF15 promotes nasopharyngeal cancer cell growth in vivo. Our study sheds light on the significance of KIF15 in NPC by revealing that KIF15 knockdown inhibits NPC cell growth through the regulation of AKT-related signaling pathways. These findings suggest that KIF15 represents a promising therapeutic target for the prevention and treatment of NPC.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.21 no.1
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• pp.1-11
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• 2018

The emergence of mucosal healing as a treatment goal that could modify the natural course of Crohn's disease and the accumulating evidence showing that biologics are most effective in achieving mucosal healing, along with the success of early treatment regimens for rheumatoid arthritis, have led to the identification of early Crohn's disease and development of the concept of catching the therapeutic window during the early disease course. Thus, an increasing number of pediatric gastroenterologists are adopting an early biologic treatment strategy with or without an immunomodulator. Although early biologic treatment is effective, cost and overtreatment are issues that limit its early use. Currently, there are insufficient data on who will benefit most from early biologics, as well as on who will not need early or even any biologics. For now, top-down biologics should be considered for patients with currently known high-risk factors of poor outcomes. For other patients, close, objective monitoring and accelerating the step-up process by means of a treat-to-target approach seems the best way to catch the therapeutic window in early pediatric Crohn's disease. The individual benefits of immunomodulator addition during early biologic treatment should be weighed against its risks and decision on early combination treatment should be made after comprehensive discussion with each patient and guardian.

• Journal of Preventive Medicine and Public Health
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• v.31 no.2 s.61
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• pp.167-182
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• 1998

The purpose of this study was to identify the major health components and measurements to be conducted in National Health Examination Survey(KNHES). The prevalence and severity of disease, acceptability of population and the possibility of standardization of measurement were considered as guideline for selecting the components. On the base of magnitude and severity of disease, chronic liver disease, hepatic cancer, gastric ulcer, stomach cancer, essential hypertension, cerebrovascular disease, ischemic heart disease, pulmonary tuberculosis, lung cancer, DM, breast cancer, cervical cancer, arthritis and intervertebral disc disorder were selected as the preliminary target diseases. Questionnaire survey for 648 persons in 'K' city and medical specialists in five clinical societies were conducted for evaluation the acceptability of general population for the measurements and the possibility of standardization for the procedures. In conclusion, the major target diseases were chronic liver disease, hypertension and DM and the total cholesterol, high density lipoprotein, triglyceride, total protein, albumin, hemoglobulin, hematocrit, platlet count, anti-HBs, HBsAg, height and weight were selected for basic physical components.