• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2006.02a
• /
• pp.46-55
• /
• 2006

(주)지노믹트리는 DNA 마이크로어레이 기술을 기반으로 하는 분자진단회사로서, 다음의 세가지 사업에 전력하고 있다. 첫째는 독창적이며 특화된 바이오마커 발굴기술 (MAGIC system)을 바탕으로 각종 암진단을 위한 바이오마커 개발연구 두 번째는 당사의 원천 기술인 다중동시검출 시스템을 이용한 질병 진단 시스템 및 증폭시스템 세 번째는 마이크로어레이 기술을 이용한 유전자 발현 분석, Array CGH, DNA 메틸레이션 분석 그리고 miRNA 검출 등의 지노믹스시대의 연구를 위한 토탈솔루션을 제공하고 있다. 지난 5년간의 마이크로어레이 기반기술을 이용한 자체연구 활동을 수행하면서 축적된 마이크로어레이 관련기술 노-하우들을 국내 마이크로어레이 연구자들에게 공급하기 위하여 노력하고 있다. 특히 당사의 지노믹서비스 부문은 유전자 발현 분석 솔루션 제공을 위해서 자체적으로 제작하여 공급하고 있는 human cDNA(17K/25K) 및 rat cDNA (5.0K) 마이크로어레이, Human (22K) 및 mouse (10K) 올리고뉴클레오타이드 마이크로 어레이 그리고 미생물 연구를 위한 대장균 (6K) 및 폐렴균 (2.2K) 올리고뉴클레오타이드 마이크로어레이 제공 및 이를 이용한 유전자 발현 분석 서비스를 제공하고 있다. 체적으로 제작되는 마이크로어레이 서비스는 2001년 도입한 ISO9001 품질인증시스템의 기반하에서 제작부터 생산까지의 엄격한 품질관리 과정을 거쳐서 고품질의 마이크로어레이를 이용한 분석서비스를 제공 하고 있다. 또한 고객요구형 서비스를 위하여 국외 유수의 마이크로어레이 회사 (Agilent, Microarray Inc, TIGR, Eurogentec 등)의 whole genome 기반의 마이크로어레이 제품을 이용한 분석서비스를 제공하고 있으며 마이크로어레이 실험을 위해서 필수적으로 이용되고 있는 시약 (labeling kit), 마이크로어레이 hybridization을 위한 hardware (hybridization chamber, hnay centrifuge)등을 자체적으로 개발하여 공급하고 있다. DNA copy number 측정을 위한 Array CGH 분석을 위해서는 자체적으로 제작공구하고 있는 human cDNA 마이크로어레이 (17K/25K) 그기고 rat (5.0K) 마이크로어레이를 이용한 분석서비스 및 whole genome 기반의 Agilent 올리고뉴클레오타이드 CGH 어레이 (44K, 35Kb resolution)를 이용한 분석서비스를 제공하고 있다. Epigenetic study를 하는 연구자들을 위한 메틸레이션 마이크로어레이 분석 서비스를 제공하고 있다. 기존분석법인 Bisulfite 처리기반의 분석이 아닌 enzyme digestion후 PCR 증폭방법을 이용한 분석방법을 이용함으로써, bisulfite 처리에 의한 DNA 손실문제를 최소화 하였다. 현재 50개의 문헌을 통해 잘 보고된 메틸레이션 유전자들에 대한 분석서비스를 제공하고 있으며, 지속적으로 표적컨텐츠의 숫자를 증가시킬 예정이다. 최근 많은 연구자들의 관심을 끌고 있는 micro RNA 검출을 위한 DNA 마이크로어레이 서비스를 제공할 예정이다 (2006년 3월 출시). 현재 까지 알려진 약 320개의 모든 miRNA를 탑재하고 있는 소형 DNA 마이크로어레이를 이용한 분석서비스로서 1장의 마이크로어레이 실험을 통하여 알려진 모든 miRNA의 비교분석이 가능하다. 마이크로어레이 실험 뿐만 아니라 data 분석을 위한 software도 상당히 중요한 비중을 차지하고 있다 이를 위하여 (주)지노믹트리는 Agilent에서 개발한 GeneSpring GX (유전자 발현 분석), Signet (마이크로어레이 database) 및 GeneSpring GT (SNP 분석)를 공급하고 있다. 통계적인 기반 지식의 없은 일반 user들을 위한 간편하면서도 종합적인 기능을 포함하고 있는 우수한 프로그램으로 이미 국제적으로 많은 인정을 받고 있다. (주)지노믹트리는 국내외 많은 연구자들의 경제적, 시간적 연구여건을 고려한 마이크로어레이 토탈솔루션을 제공하고 있으며, 실험 분석에서 data 마이닝 그리고 마이크로어레이 실험 디자인에 이르는 토탈솔루션을 제공하고 있다.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.11
• /
• pp.5405-5408
• /
• 2012

Curcumin (CM), a biphenyl compound, possesses anti-inflammatory, antioxidant and antimicrobial activity. MicroRNAs (miRNAs) are small noncoding RNAs which regulate gene expression and the molecular mechanisms of several biological processes. Liver fibrosis is a major cause of hepatic dysfunction and cancer and there are few effective therapies emphasizing the need for new approaches to control. The present study was conducted to investigate the effect of curcumin (CM) on liver fibrosis through modulating the expression level of miRNAs (199 and 200), the main miRNAs associated with liver fibrosis. Induction of liver fibrosis by carbon tetrachloride ($CCL_4$) was confirmed by histopathological examination. Mice were divided into 3 groups: group 1 were i.p injected with 10% $CCL_4$ twice weekly for 4 weeks and then once a week for the next 4 weeks followed by 4 weeks with olive oil only. Group 2 were i.p injected with 10% $CCL_4$ twice weekly for 4 weeks and then once a week for the next 4 weeks followed by curcumin (5 mg/mouse/day) once daily for the next 4 weeks. The third group was injected with olive oil. The expression level of miR-199 and miR-200 and some of their targeted genes were measured by real time PCR. miRNA (199 and 200) levels were significantly elevated in liver fibrotic tissues compared to control groups. Curcumin was significantly returned the expression levels of mir-199 and -200 with their associated target gene nearly to their normal levels. This is the first study that highlighted the effect of curcumin on liver fibrosis through regulation of miRNAs.

• The Journal of Advanced Prosthodontics
• /
• v.11 no.6
• /
• pp.341-349
• /
• 2019

PURPOSE. A novel retentive type of implant prosthesis that does not require the use of cement or screw holes has been introduced; however, there are few reports examining the biomechanical aspects of this novel implant. This study aimed to evaluate the biomechanical features of cementless fixation (CLF) implant prostheses. MATERIALS AND METHODS. The test groups of three variations of CLF implant prostheses and a control group of conventional cement-retained (CR) prosthesis were designed three-dimensionally for finite element analysis. The test groups were divided according to the abutment shape and the relining strategy on the inner surface of the implant crown as follows; resin-air hole-full (RAF), resin-air hole (RA), and resin-no air hole (RNA). The von Mises stress and principal stress were used to evaluate the stress values and distributions of the implant components. Contact open values were calculated to analyze the gap formation of the contact surfaces at the abutment-resin and abutment-implant interfaces. The micro-strain values were evaluated for the surrounding bone. RESULTS. Values reflecting the maximum stress on the abutment were as follows (in MPa): RAF, 25.6; RA, 23.4; RNA, 20.0; and CR, 15.8. The value of gap formation was measured from 0.88 to 1.19 ㎛ at the abutment-resin interface and 24.4 to 24.7 ㎛ at the abutment-implant interface. The strain distribution was similar in all cases. CONCLUSION. CLF had no disadvantages in terms of the biomechanical features compared with conventional CR implant prosthesis and could be successfully applied for implant prosthesis.

• BMB Reports
• /
• v.52 no.3
• /
• pp.202-207
• /
• 2019

Keloids are the most common pathological form of trauma healing, with features that seriously affect appearance and body function, are difficult to treat and have a high recurrence rate. Emerging evidence suggests that miRNAs are involved in a variety of pathological processes and play an important role in the process of fibrosis. In this study, we investigated the function and regulatory network of miR-152-5p in keloids. The miRNA miR-152-5p is frequently downregulated in keloid tissue and primary cells compared to normal skin tissue and fibroblasts. In addition, the downregulation of miR-152-5p is significantly associated with the proliferation, migration and apoptosis of keloid cells. Overexpression of miR-152-5p significantly inhibits the progression of fibrosis in keloids. Smad3 is a direct target of miR-152-5p, and knockdown of Smad3 also inhibits fibrosis progression, consistent with the overexpression of miR-152-5p. The interaction between miR-152-5p and Smad3 occurs through the Erk1/2 and Akt pathways and regulates collagen3 production. In summary, our study demonstrates that miR-152-5p/Smad3 regulatory pathways involved in fibrotic progression may be a potential therapeutic target of keloids.

• IMMUNE NETWORK
• /
• v.22 no.6
• /
• pp.49.1-49.15
• /
• 2022

Exosomes derived from mesenchymal stem cells (MSCs) could protect against myocardial infarction (MI). TLR4 is reported to play an important role in MI, while microRNA-182-5p (miR-182-5p) negatively regulates TLR4 expression. Therefore, we hypothesize that MSCs-derived exosomes overexpressing miR-182-5p may have beneficial effects on MI. We generated bone marrow mesenchymal stem cells (BM-MSCs) and overexpressed miR-182-5p in these cells for exosome isolation. H₂O₂-stimulated neonatal mouse ventricle myocytes (NMVMs) and MI mouse model were employed, which were subjected to exosome treatment. The expression of inflammatory factors, heart function, and TLR4 signaling pathway activation were monitored. It was found that miR-182-5p decreased TLR4 expression in BM-MSCs and NMVMs. Administration of exosomes overexpressing miR-182-5p to H₂O₂-stimulated NMVMs enhanced cell viability and suppressed the expression of inflammatory cytokines. In addition, they promoted heart function, suppressed inflammatory responses, and de-activated TLR4/NF-κB signaling pathway in MI mice. In conclusion, miR-182-5p transferred by the exosomes derived from BM-MSCs protected against MI-induced impairments by targeting TLR4.

• ALGAE
• /
• v.39 no.1
• /
• pp.43-50
• /
• 2024

Oomycetes are ubiquitous heterotrophs of considerable economic and ecological importance. Lately their diversity in marine environments has been shown to be greatly underappreciated and many lineages of intracellular holocarpic parasites, infecting micro- and macro-algae, remain to be fully described taxonomically. Among them, pathogens of marine red algae have been studied extensively as they infect important seaweed crops. Throughout the 20th century, most intracellular, holocarpic biotrophic oomycetes that infect red algae have been assigned to the genus Olpidiopsis Cornu. However, 18S rRNA sequencing of Olpidiopsis saprolegniae, the species considered the generitype for Olpidiopsis, suggests that this genus is not closely related to the marine pathogens and that the latter requires a nomenclatural update. Here, we compile and reanalyze all recently published 18S rRNA sequence data for marine holocarpic oomycetes, with a particular focus on holocarpic pathogens of red algae. Their taxonomy has been revised twice over the past four years, with suggestions to transfer them first into the genus Pontisma and then Sirolpidium, and into a monogeneric order, Pontismatales. We show however, that previously published topologies and the proposed taxa Pontisma, Sirolpidium, and Pontismatales are unsupported. We highlight that name changes that are unfounded and premature create confusion in interested parties, especially concerning pathogens of marine red algae that infect important seaweed crops. We thus propose that the names of these holocarpic biotrophic parasites of red algae are retained temporarily, until a supported topology is produced with more genetic markers to enable the circumscription of species and higher-level taxa.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
• /
• v.46 no.5
• /
• pp.341-347
• /
• 2020

Objectives: Oral squamous cell carcinoma (OSCC) is one of the most common types of head and neck cancer. MicroRNAs, as new biomarkers, are recommended for diagnosis and treatment of different types of cancers. Bevacizumab, sold under the trade name Avastin, is a humanized whole monoclonal antibody that targets and blocks VEGF-A (vascular endothelial growth factor A; angiogenesis) and oncogenic signaling pathways. Materials and Methods: This study comprised 50 cases suffering from OSCC and 50 healthy participants. Peripheral blood samples were collected in glass test tubes, and RNA extraction was started immediately. Expression levels of miR-155, miR-191, and miR-494 biomarkers in the peripheral blood of OSCC-affected individuals and healthy volunteers in vivo were evaluated using real-time PCR. The influence of Avastin on the expression levels of the aforementioned biomarkers in vitro and in the HN5 cell line was also investigated. Results: Expression levels of miR-155, miR-191, and miR-494 in the peripheral blood of individuals affected by OSCC were higher than in those who were healthy. Moreover, Avastin at a concentration of 400 μM caused a decrease in the expression levels of the three biomarkers and a 1.5-fold, 3.5-fold, and 4-fold increase in apoptosis in the test samples compared to the controls in the HN5 cell line after 24, 48, and 72 hours, respectively. Conclusion: The findings of this study demonstrate that overexpression of miR-155, miR-191, and miR-494 is associated with OSCC, and Avastin is able to regulate and downregulate the expression of those biomarkers and increase apoptosis in cancerous cells in the HN5 cell line.

• Molecules and Cells
• /
• v.41 no.9
• /
• pp.868-880
• /
• 2018

Pancreatic cancer (PC) is one of the most aggressive cancers presenting with high rates of invasion and metastasis, and unfavorable prognoses. The current study aims to investigate whether EZH2/miR-139-5p axis affects epithelial-mesenchymal transition (EMT) and lymph node metastasis (LNM) in PC, and the mechanism how EZH2 regulates miR-139-5p. Human PC and adjacent normal tissues were collected to determine expression of EZH2 and miR-139-5p, and their relationship with clinicopathological features of PC. Human PC cell line was selected, and treated with miR-139-5p mimics/inhibitors, EZH2 vector or shEZH2 in order to validate the regulation of EZH2-mediated miR-139-5p in PC cells. Dual-luciferase report gene assay and chromatin immunoprecipitation assay were employed to identify the relationship between miR-139-5p and EZH2. RT-qPCR and Western blot analysis were conducted to determine the expression of miR-139-5p, EZH2 and EMT-related markers and ZEB1/2. Tumor formation ability and in vitro cell activity were also analyzed. Highly-expressed EZH2 and poorly-expressed miR-139-5p were detected in PC tissues, and miR-139-5p and EZH2 expressions were associated with patients at Stage III/IV, with LNM and highly-differentiated tumors. EZH2 suppressed the expression of miR-139-5p through up-regulating Histone 3 Lysine 27 Trimethylation (H3K27me3). EMT, cell proliferation, migration and invasion were impeded, and tumor formation and LNM were reduced in PC cells transfected with miR-139-5p mimics and shEZH2. MiR-139-5p transcription is inhibited by EZH2 through up-regulating H3K27me3, thereby down-regulation of EZH2 and up-regulation of miR-139-5p impede EMT and LNM in PC. In addition, the EZH2/miR-139-5p axis presents as a promising therapeutic strategy for the treatment of PC.

• BMB Reports
• /
• v.42 no.9
• /
• pp.552-560
• /
• 2009

Cyclooxygenases (COX-1 and COX-2) are ER-resident proteins that catalyze the committed step in prostanoid synthesis. COX-1 is constitutively expressed in many mammalian cells, whereas COX-2 is usually expressed inducibly and transiently. Abnormal expression of COX-2 has been implicated in the pathogenesis of chronic inflammation and various cancers; therefore, it is subject to tight and complex regulation. Differences in regulation of the COX enzymes at the posttranscriptional and posttranslational levels also contribute significantly to their distinct patterns of expression. Rapid degradation of COX-2 mRNA has been attributed to AU-rich elements (AREs) at its 3’UTR. Recently, microRNAs that can selectively repress COX-2 protein synthesis have been identified. The mature forms of these COX proteins are very similar in structure except that COX-2 has a unique 19-amino acid (19-aa) segment located near the C-terminus. This C-terminal 19-aa cassette plays an important role in mediation of the entry of COX-2 into the ER-associated degradation (ERAD) system, which transports ER proteins to the cytoplasm for degradation by the 26S proteasome. A second pathway for COX-2 protein degradation is initiated after the enzyme undergoes suicide inactivation following cyclooxygenase catalysis. Here, we discuss these molecular determinants of COX-2 expression in detail.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.1
• /
• pp.17-24
• /
• 2014

Gastric cancer is highly invasive, aggressively malignant, and amongst the most prevalent of all forms of cancer. Despite improved management strategies, early stage diagnosis of gastric cancer and accurate prognostic assessment is still lacking. Several recent reports have indicated that the pathogenesis of gastric cancer involves complex molecular mechanisms and multiple genetic and epigenetic alterations in oncogenes and tumor suppressor genes. Functional inactivation of the tumor suppressor protein PTEN (Phosphatase and Tensin Homolog) has been detected in multiple cases of gastric cancer, and already shown to be closely linked to the development, progression and prognosis of the disease. Inactivation of PTEN can be attributed to gene mutation, loss of heterozygosity, promoter hypermethylation, microRNA- mediated regulation of gene expression, and post-translational phosphorylation. PTEN is also involved in mechanisms regulating tumor resistance to chemotherapy. This review provides a comprehensive analysis of PTEN and its roles in gastric cancer, and emphasizes its potential benefits in early diagnosis and gene therapy-based treatment strategies.