Novel Methylation Biomarker for Non-invasive Diagnostics in Lung Cancer

오태정,( Chang Hun Lee2 ),( Min Ki Lee ),( Yeul Hong Kim ),( Sang Yull Lee ),( Hyo Sung Jeon ),( Shin Yup Lee ),( Seung Soo Yoo ),( Jae Yong Park ),( Sung Whan An ) 대한결핵 및 호흡기학회 2012 대한결핵 및 호흡기학회 추계학술대회 초록집 Vol.114 No.-

To identify aberrantly hypermethylated DNA in lung cancer cells we established a genome-wide analysis for hypermethylation sites, namely Methyl DNA Isolation and Amplification (MeDIA) coupled-CpG microarray analysis. In the comprehensive methyaltion profiling analysis between human lung cancer, A549 cells and normal NHBE cells, we observed that several clusters of genes show a significant level of aberrancy in CpG island methylation pattern in cancer cells compared to normal cells. We further identified PCDHGA12 gene as a new marker of non-invasive diagnostics for lung cancer based on followings. 1) Transcription of PCDHGA12 gene is reactivated after treatment of A549 cells with demethylating agent. 2) Bisulfide clonal-sequencing reveals that CpG island of PCDHGA12 shows a distinctive differential methylation between two cell lines. 3) Pyrosequencing-based quantitative methylation assay for such region in tumor and non-tumorous tissues from lung cancer patients shows aberrant hypermethylation in 37 (92%) of the 40 tumor tissues. In clinical validation by pyrosequencingin induced-sputum of lung cancer patients (n=87) and healthy controls (n=51), we observed aberrant hypermethylation incident at significantly elevated level in samples derived from lung cancer patients. According to the optimal threshold calculated by ROC curve analysis, sensitivity and specificity of PCDHGA12 was 86.2% and 82.4%, respectively. PCDHGA12 methylation status could be a potential methylation biomarker alone or combined with others for the screen and the detection of relapse of lung cancer.

Redislocation after Bearing Exchange for the Treatment of Mobile Bearing Dislocation in Medial Unicompartmental Knee Arthroplasty

( Sang-gyun Kim ),( Hyun-gon Kim ),( Seung-yup Lee ),( Hong-chul Lim ),( Ji-hoon Bae ) 대한슬관절학회 2018 대한슬관절학회지 Vol.30 No.3

Purpose: This study was conducted to investigate the outcomes of bearing exchange for the treatment of mobile bearing dislocation in medial unicompartmental knee arthroplasty (UKA). Materials and Methods: We retrospectively reviewed 18 patients (15 females and 3 males, mean age of 65 years) treated with bearing exchange following mobile bearing dislocation in medial UKA. The occurrence of bearing redislocation, the Oxford Knee Score, and radiographic changes at the last follow-up were investigated. Results: Bearing redislocation after bearing exchange occurred in 9 of 18 patients (50%). Of these 9 patients, 7 underwent conversion to total knee arthroplasty after bearing redislocation. The 9 patients without bearing redislocation showed good to excellent clinical outcomes at a mean followup of 55 months after bearing exchange. The non-redislocation group had a higher percentage of posterior dislocation of the bearing than the redislocation group (55.5% vs. 22.2%, p=0.040). Univariate logistic regression analysis showed no significant risk factors for bearing redislocation. Conclusions: This study showed a high rate of bearing redislocation after isolated, mobile bearing exchange for bearing dislocation following medial UKA. Therefore, bearing exchange as a sole treatment should be carefully considered in selected patients with correctable causes of bearing dislocation.

A Case of Facial Nerve Schwannoma Presenting as an External Auditory Canal Mass

Sang Heun Lee,정다정,Jun Ho Seok,Kyu Yup Lee 대한청각학회 2011 Journal of Audiology & Otology Vol.15 No.3

Introduction Benign tumors, which originate from the peripheral nerve sheath that surrounds the axons of peripheral nerves, can be divided into two major groups: schwannoma and neurofibroma.1) Schwannoma is a tumor that originates from Schwann cells in the peripheral neurilemma, and approximately 25 percent of these tumors are known to occur in the head and neck region.2,3) The prevalence rate of facial nerve schwannomas is 1/23,000,4) and facial nerve schwannomas on the external temporal bone have been reported in 15% of all cases.5) The occurrence of facial nerve schwannomas in the middle ear and mastoid cavity is relatively rare. We report here on a case of schwannoma that originated from the mastoid segment of the facial nerve, which was presented as external auditory canal mass. Case Report A 24-year-old male patient presented to us a symptom in the right ear fullness, which had been occurring for a year. The ear fullness was felt only in the morning at first, but the pain had become severe in the last two to three months ago, and lasted all day. When he visited our hospital, there was a House- Brackmann Grade II facial nerve paralysis, and polyp-formed mass with a smooth surface that had filled the right external auditory canal. The eardrum could not be found due to the mass (Fig. 1). In pure-tone audiometry of 500 Hz, 1,000 Hz and 2,000 Hz, the right ear had an air conduction threshold of 35 dB HL and bone conduction threshold of 5 dB. In addition, the air-bone gap was 30 dB. In the computed tomography (CT) scan of the temporal bone, a shade of soft tissue that filled some of external auditory canal and mastoid was connected to the stylo-mastoid foramen. There were defects on the posterior wall of the external auditory canal due to the mass, but there were no specific ossicles and tympanic segment found on the facial nerve (Fig. 2). In the magnetic resonance image (MRI) T1 weighted image, the same relative signal strength and contrast enhancement with the brain parenchyma was observed and the mass, which was 1.3×1.4 cm, was connected to the part of the mastoid and stylo-mastoid foramen, through the external auditory canal (Fig. 3). It was diagnosed as schwannoma in preoperative incisional biopsy results, which were positive for S-100 protein staining. The dia-gnosis was facial nerve neurilemmoma, which caused the conductive hearing loss and invaded the entire external auditory canal and the middle ear. Surgery was performed using the transmastoid approach. The mass in the external auditory canal was connected to the part of the epitympanum and the mastoid cavity, along the posterior wall of external auditory canal. The mass started at the second genu of the facial nerve, and was connected to the stylomastoid foramen across the entire mastoid segments. However, It had a distinct border with the tympanic segment, so it was relatively easy to dissect. After resection of the mass, neurorraphy with the great auricular nerve was performed using a 9-0 nylon suture. After Tissue glue (Tisseel kit® 2 mL, Baxter) was applied to the connected nerves, we covered the nerves with tragal cartilage, tragal perichondrium and temporalis muscle fascia, and obliterated the opening with an inferior based musculocutaneous flap (Fig. 4). Keratin had gathered began to form a cholesteatoma in the external auditory canal that was inside of the mass. In addition, part of the tympanic membrane was lost due to the mass but the ossicles were intact. In the histopathologic report, Antoni type A, which are the spindle cells, and the surrounding connective tissues were well-arranged, and Antoni type B, which has relatively loose phlegmatic temparament, were scattered. Thus, this case was diagnosed as a typical schwannoma, which was positive for S-100 protein staining (Fig. 5). He had no symptoms such as dizziness after the surgery. It has been 3 months since the surgery and the facial nerve palsy of patients is House-Brackmann Grade III (... Facial nerve schwannoma is a rare benign tumor that arises from the Schwann cell sheath of facial nerve. Although the tumor can occur anywhere along the course of the peripheral nerve, it is frequently present as an internal auditory canal mass in the head and neck region. We experienced a rare case of facial nerve schwannoma on the mastoid segment, which was presented as an external auditory canal mass in a 24-years-old man. The lesion was removed via the transmastoid approach and the facial nerve was grafted using the greater auricular nerve. The patient's facial nerve function was preserved postoperatively as House-Brackmann grade III

Microcontact Printing of Biotin for Selective Immobilization of Streptavidin-fused Proteins and SPR Analysis

Lee, Sang-Yup,Park, Jong-Pil,Lee, Seok-Jae,Park, Tae-Jung,Lee, Kyung-Bok,Park, Insung S.,Kim, Min-Gon,Chung, Bong-Hyun The Korean Society for Biotechnology and Bioengine 2004 Biotechnology and Bioprocess Engineering Vol.9 No.2

In this study, a simple procedure is described for patterning biotin on a glass substrate and then selectively immobilizing proteins of interest onto the biotin-patterned surface. Microcontact printing (CP) was used to generate the micropattern of biotin and to demonstrate the selective immobilization of proteins by using enhanced green fluorescent protein (EGFP) as a model protein, of which the C-terminus was fused to a core streptavidin (cSA) gene of Streptomyces avidinii. Confocal fluorescence microscopy was used to visualize the pattern of the immobilized protein (EGFP-cSA), and surface plasmon resonance was used to characterize biological activity of the immobilized EGFP-cSA. The results suggest that this strategy, which consists of a combination of $\mu$CP and cSA-fused proteins. is an effective way for fabricating biologically active substrates that are suitable for a wide variety of applications. one such being the use in protein-protein assays.

Systems-Level Analysis of Genome-Scale In Silico Metabolic Models Using MetaFluxNet

Lee, Sang-Yup,Woo, Han-Min,Lee, Dong-Yup,Choi, Hyun-Seok,Kim, Tae-Yong,Yun, Hong-Seok The Korean Society for Biotechnology and Bioengine 2005 Biotechnology and Bioprocess Engineering Vol.10 No.5

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

Benchmarking Studies for Template-Based Modeling of Protein Structures

Sang Mi LEE,Woo Dae JANG,Hyun Uk KIM,Sang Yup LEE 한국생물공학회 2019 한국생물공학회 학술대회 Vol.2019 No.10

Cloning and Characterization of Mannheimia succiniciproducens MBEL55E Phosphoenolpyruvate Carboxykinase (pckA) Gene

Lee, Sang-Yup,Lee, Pyung-Cheon,Hong, Soon-Ho,Chang, Ho-Nam The Korean Society for Biotechnology and Bioengine 2002 Biotechnology and Bioprocess Engineering Vol.7 No.2

A pckA gene encoding phosphoenolpyruvate carboxykinase (PEPCK) was cloned and sequenced from the succinic acid producing bacterium Mannheimia succiniciproducens MBEL55E. The gene encoded a 538 residue polypeptide with a calculated molecular mass of 58.8 kDa and a calculated pI of 5.03. The deduced amino acid sequence of the M. succiniciprodutens MBEL55E PEPCK was similar to those of all known ATP-dependent PEPCKS.

Change Analysis and Development Direction of BK21 PLUS Project : Focusing on Social Big Data Analysis

Sung-Jun Myung,Yeon-Soo Kim,Sang-Yup Lee 한국자치행정학회 2017 한국자치행정학보 Vol.31 No.4

대학교육의 사명과 역할, 대학교육의 내용과 방법에도 근본적인 변화가 나타나고 있다. 이러한 대학교육의 환경과 체질 변화 속에서 이제는 우리가 원하는 대학교육의 모습은 어떠한지, 대학교육을 어떻게 발전시킬 것인지, 그러한 발전을 위해서는 대학교육 재정지원이 어떤 방향으로 변화되어야 하는지에 관해서 좀 더 근본적인 성찰이 필요하고, 장기적인 구상과 세밀한 설계도를 마련해야 할 시점이다. 대학지원정책으로서 BK21 PLUS(Brain Korea 21 PLUS)는 학자 및 언로 등에 의해 많이 분석되어 왔다. 최근 스마트기기의 급속한 보급과 소셜미디어의 확산으로 자료의 양이 기하급수적으로 증가하고 데이터의 생산, 유통, 소비 체계에 큰 변화를 주면서 데이터가 경제적 자산이 될 수 있는 빅데이터 시대를 맞이하게 됨에 따라 정부 정책에 대한 국민들의 인식을 소셜 빅 데이터 분석을 통해 분석할 필요가 있다. 본 논문에서는 대학재정지원사업, 특히 연구중심대학지원사업인 BK21 PLUS Project를 중심으로 소셜 빅 데이터분석을 통해 사업의 변화를 분석하고, 이 사업의 발전방향을 탐색적 차원에서 제시하였다. 분석의 함의는 2021년에 새로 시작될 가칭 BK21 FOUR 사업에서는 전체 대학 중 상위 15% 이내 대학만 선정이 가능하도록 해서 연구중심대학으로서의 차별화를 시도해야 한다. 첫째, 인재양성 측면에서, 고등교육의 선순환적 자생생태계를 구축해야 한다. 인력 양성 및 활용의 선순환 생태계 구축을 위한 시스템을 설계하고, 인재 활용방안을 고도화해야 한다. 둘째, 연구경쟁력 측면에서, 양질의 균형 잡힌 연구역량 강화를 위한 노력이 이어져야 한다. 자율적 경쟁을 강화하고, 연구경쟁력 강화를 위한 사업단 중심의 개편 작업이 이루어져야 한다. Fundamental changes are also emerging from the missions and roles in the university education and the contents and methods in the university education. In the changes of environments and constitutions in this university education, now is the time when more fundamental reflection is required and long-term and detailed plans are established regarding what is the image of university that people want, how to develop university education and how the financial support for university education should be changed. Meanwhile, BK21 PLUS (Brain Korea 21 PLUS) has been analyzed through the reports and related press releases. Recently, as smart devices and social media spread out rapidly, the amount of data is increasing exponentially and Big Data Age arrives where the data can become an economic asset while making big changes in data production, distribution and consumption, now is the time to analyze the public awareness about the government policy through social big data analysis. Therefore, this paper analyzed the changes of the project through the analysis of social big data focusing on the university financial support project, especially on BK21 PLUS Project which is a research-oriented university support project, and presented the development direction of this project in an exploratory level. In the tentative BK21 FOUR project which will newly start in 2021, differentiation is required to select only the top 15% of universities as research-oriented university. First, in the aspects of human resource development, a virtuous autogenous ecosystem should be established for higher education. A system should be designed to construct virtuous ecosystem and utilization plans of manpower should be improved. Second, in the aspects of research competitiveness, efforts should be made to strengthen the quality of balanced research competence. In order to strengthen autonomous competition and research competitiveness, project reorganization should be made focusing on project teams.

Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars

Lee, Yun Sun,Park, Hyun-Seung,Lee, Dong-Kyu,Jayakodi, Murukarthick,Kim, Nam-Hoon,Lee, Sang-Choon,Kundu, Atreyee,Lee, Dong-Yup,Kim, Young Chang,In, Jun Gyo,Kwon, Sung Won,Yang, Tae-Jin The Korean Society of Ginseng 2017 Journal of Ginseng Research Vol.41 No.1

Background: Various Panax ginseng cultivars exhibit a range of diversity for morphological and physiological traits. However, there are few studies on diversity of metabolic profiles and genetic background to understand the complex metabolic pathway in ginseng. Methods: To understand the complex metabolic pathway and related genes in ginseng, we tried to conduct integrated analysis of primary metabolite profiles and related gene expression using five ginseng cultivars showing different morphology. We investigated primary metabolite profiles via gas chromatography-mass spectrometry (GC-MS) and analyzed transcriptomes by Illumina sequencing using adventitious roots grown under the same conditions to elucidate the differences in metabolism underlying such genetic diversity. Results: GC-MS analysis revealed that primary metabolite profiling allowed us to classify the five cultivars into three independent groups and the grouping was also explained by eight major primary metabolites as biomarkers. We selected three cultivars (Chunpoong, Cheongsun, and Sunhyang) to represent each group and analyzed their transcriptomes. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways. Conclusion: Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.

Clinical and molecular characterizations of novel POU3F4 mutations reveal that DFN3 is due to null function of POU3F4 protein.

Lee, Hee Keun,Song, Mee Hyun,Kang, Myengmo,Lee, Jung Tae,Kong, Kyoung-Ah,Choi, Su-Jin,Lee, Kyu Yup,Venselaar, Hanka,Vriend, Gert,Lee, Won-Sang,Park, Hong-Joon,Kwon, Taeg Kyu,Bok, Jinwoong,Kim, Un-Kyun American Physiological Society 2009 PHYSIOLOGICAL GENOMICS Vol.39 No.3

<P>X-linked deafness type 3 (DFN3), the most prevalent X-linked form of hereditary deafness, is caused by mutations in the POU3F4 locus, which encodes a member of the POU family of transcription factors. Despite numerous reports on clinical evaluations and genetic analyses describing novel POU3F4 mutations, little is known about how such mutations affect normal functions of the POU3F4 protein and cause inner ear malformations and deafness. Here we describe three novel mutations of the POU3F4 gene and their clinical characterizations in three Korean families carrying deafness segregating at the DFN3 locus. The three mutations cause a substitution (p.Arg329Pro) or a deletion (p.Ser310del) of highly conserved amino acid residues in the POU homeodomain or a truncation that eliminates both DNA-binding domains (p.Ala116fs). In an attempt to better understand the molecular mechanisms underlying their inner ear defects, we examined the behavior of the normal and mutant forms of the POU3F4 protein in C3H/10T1/2 mesodermal cells. Protein modeling as well as in vitro assays demonstrated that these mutations are detrimental to the tertiary structure of the POU3F4 protein and severely affect its ability to bind DNA. All three mutated POU3F4 proteins failed to transactivate expression of a reporter gene. In addition, all three failed to inhibit the transcriptional activity of wild-type proteins when both wild-type and mutant proteins were coexpressed. Since most of the mutations reported for DFN3 thus far are associated with regions that encode the DNA binding domains of POU3F4, our results strongly suggest that the deafness in DFN3 patients is largely due to the null function of POU3F4.</P>