Application of NanoString technologies in angioimmunoblastic T-cell lymphoma

Wonseok Shin,Seyoung Mun,Seungkyu Choi,Kyudong Han 한국유전학회 2020 Genes & Genomics Vol.42 No.4

Background Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive disease. Most cancer diagnoses are determined by anatomical histology. Therefore, many samples are stored in FFPE blocks for H&E staining. However, RNAs extracted from the FFPE block have a high level of fragmentation, making it difficult to perform accurate DEG analysis using RNA sequencing. Objective To overcome fragmented RNA’s drawback in NGS application, we applied the NanoString nCounter® technique of hybridization method that can be used for DEG analysis without PCR amplification. Methods We characterized the gene expression profiling of AITLs though transcriptome analysis based on the nCounter® PanCancer IO 360™ Panel and NanoString platform. To perform the analysis of differential expression gene (DEG) profiles in AITLs, we compared the NanoString data from eight AITL patients with a healthy control donor. Results Ninety-one genes were up-regulated and six genes were down-regulated in AITLs compared to control. The Gene Ontology (GO) analysis of 97-DEGs revealed that they were closely related to cytokine, MAPK cascade, leukocyte differentiation, and immune response, suggesting that this affect the immune system. In addition, KEGG analysis revealed that AITL DEGs were found to be highly involved in cytokine–cytokine receptor interaction and PI3K-Akt signaling pathway. Conclusion We believe that comprehensive multiplex studies, along with NanoString analysis, may be helpful to understand the molecular mechanisms of AITL, including mutations, gene expression, and protein expression studies.

Quantitative evaluation of the molecular marker using droplet digital PCR

Shin, Wonseok,Kim, Haneul,Oh, Dong-Yep,Kim, Dong Hee,Han, Kyudong Korea Genome Organization 2020 Genomics & informatics Vol.18 No.1

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.

Comparison of genetic variation between primary colorectal cancer and metastatic peritoneal cancer

Shin Wonseok,Yun Jeongseok,Han Kyudong,Park Dong-Guk 한국유전학회 2023 Genes & Genomics Vol.45 No.8

Background Among cancer metastases by primary colorectal cancer (CRC), peritoneal metastasis is the second most common metastatic lesion after liver metastasis. In treating metastatic CRC, it is very important to differentiate targeted-therapy and chemotherapy according to the characteristics of each lesion because the genetic variation of the primary and metastatic lesions are different. However, there are few studies of genetic characteristics on peritoneal metastasis caused by primary CRC, so molecular-level studies are continuously required. Objective We propose an appropriate peritoneal metastasis treatment policy by identifying the genetic characteristics between primary CRC and synchronous peritoneal metastatic lesions. Methods Primary CRC and synchronous peritoneal metastasis samples were analyzed in pairs from six patients using Comprehensive Cancer Panel (409 cancer-related genes, Thermo Fisher Scientific, USA) and next-generation sequencing (NGS). Results The mutations were commonly found on the KMT2C and THBS1 genes in both primary CRC and peritoneal metastasis. The PDE4DIP gene was mutated in all cases except for on a sample of peritoneal metastasis. As a result of analysis using the mutation database, we confirmed that the gene mutations of primary CRC and the peritoneal metastasis derived from it showed the same tendency, although we did not accompany the gene expression level or epigenetic study. Conclusion It is thought that the treatment policy through molecular genetic testing of primary CRC can also be applied to peritoneal metastasis treatment. Our study is expected to be the basis for further peritoneal metastasis research.

Rapid identification of SARS-CoV-2 in the point-of-care using digital PCR-based Dr. PCR™ Di20K COVID-19 Detection Kit without viral RNA extraction

Shin Wonseok,Lee Cherl-Joon,Lee Yong-Moon,Choi Young-Bong,Mun Seyoung,Han Kyudong 한국유전학회 2022 Genes & Genomics Vol.44 No.5

Background: Since COVID-19 was declared the pandemic by the WHO, it has continued to spread. There is a need for rapid, efficient, and accurate diagnostic kits and techniques to control its spread. Objective: The diagnostic capability of the qRT-PCR-based Real-Q 2019-nCoV Detection Kit and dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit was compared and evaluated. Methods: Diagnostic tests for COVID-19 were performed using two different COVID-19 kits and 301 individual specimens with confirmed COVID-19 positive/negative at the government-accredited medical institution. Assessment of diagnostic capability was measured through diagnostic sensitivity, specificity, Cohen's Kappa coefficient, and dilutional linearity tests. Results: The COVID-19 diagnostic test results using two kits and 301 individual specimens perfectly matched the pre-diagnosis results of the medical institution. In addition, the measurement results of diagnostic sensitivity and specificity were "1", indicating high diagnostic capability. Cohen's Kappa coefficient value is "1", which means that the diagnosis concordance between the two kits is "Almost Perfect". As a result of dilutional linearity tests to evaluate their detection capability, both kits were measured with very high detection reliability. Conclusion: Here, we propose that the dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit has the advantages of the dPCR method reported in the previous study and is suitable for point-of-care testing (POCT) by overcoming the limitations of space, test time, cross-over contamination, and biosafety due to omitting RNA extraction process.

Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method

Shin, Wonseok,Mun, Seyoung,Kim, Junse,Lee, Wooseok,Park, Dong-Guk,Choi, Seungkyu,Lee, Tae Yoon,Cha, Seunghee,Han, Kyudong Korean Society for Molecular and Cellular Biology 2019 Molecules and cells Vol.42 No.1

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

HCV, Acute, LT : Hepatitis C Virus Attenuates Interferon-Induced Mhc Class I Expression to CIRCUMVENT CD8+ T Cell Responses

( Wonseok Kang ),( Sarah Yoon ),( Pil Soo Sung ),( Dong Yeop Chang ),( Seungtaek Kim ),( Kwang Hyub Han ),( Ja Kyung Kim ),( Yong Joon Chwae ),( Eui Cheol Shin ) 대한간학회 2013 춘·추계 학술대회 (KASL) Vol.2013 No.1

Background: Major histocompatibility complex (MHC) classI-restricted CD8+ T cells are crucial for the clearance of hepatitisC virus (HCV) infection. MHC class I expression is upregulatedby type I, and II interferons (IFNs) which are producedduring HCV infection. However, the effect of HCV infectionon IFN-induced MHC class I expression remains elusive.Methods: Using an in vitro HCV infection system, IFN-inducedMHC class I expression and its regulatory mechanismswere investigated by flow cytometry, metabolic labeling, immunoprecipitationand immunoblotting. Protein kinase R(PKR) was knocked-down using shRNA-lentiviruses. Thefunctional implication of MHC class I regulation by HCV wasdemonstrated by a co-culture study using HCV-infected cellsand HCV-specific CD8+ T cells.Results: While the baseline level of MHC class I was not affectedby HCV infection, IFN-induced MHC class I expressionwas notably attenuated in HCV-infected cells. This was associatedwith the replicating HCV RNA, not with the viral proteinper se. HCV infection diminished IFN-induced synthesis ofMHC class I protein and induced phosphorylation of PKR andeIF2α. IFN-induced MHC class I expression was restored byPKR-silencing in HCV-infected cells. In addition, a co-culturestudy using HCV-specific CD8+ T cells and HCV-infectedHLA-A2-expressing cells demonstrated that HCV infection diminishedthe effector functions of HCV-specific CD8+ T cells,which were recovered by PKR-silencing.Conclusions: IFN-induced MHC class I expression is attenuatedby HCV infection through PKR activation, which leads toa reduction of the antiviral effector functions of HCV-specific CD8+ T cells. Herein, we report a novel mechanism by which HCV circumvents antiviral adaptive immune responses.

An Analysis of Private Equity Funds in Korea and Their Role in the Korean Economy in the Post-Crisis Period

SHIN, JIYEON,WOO, WONSEOK Institute for International Trade and Cooperation 2008 Asian International Studies Review Vol.9 No.1

This paper aims to argue that private equity funds play a critical role in the Korean economy and that their presence, now and in the future is essential. Moreover, domestic private equity funds will be complementary to foreign private equity funds, not a substitute, at least for the time being. In arguing so, we will look into the investment experiences of foreign private equity funds and see how foreign private equity funds have helped transform the economy in the post-financial crisis era. We will also look at the domestic private equity funds market to examine the replicability of private equity-driven growth in Korea. The paper will conclude with further recommendations for the growth of the private equity market. In the past five years or so, Koreans have come to be familiar with names such as Carlyle, Newbridge Capital, Lone Star, etc. These are the names of major foreign institutional investment firms that bought out the Korean domestic banks, Koram Bank, Korea First Bank, and Korea Exchange Bank. Recently, with the incident of the Lone Star scandal disclosed in regards to its acquisition of Korea First Bank, the Korean media have given extensive coverage to the issues relating to private equity funds. Especially after the scandals involving foreign investors, there is public discontent about the large volume of oreign private equity funds, mainly in the financial sector, that seem to 'eat and run' once increased profits have been made. People have scrutinized investments of this kind with critical eyes. Nevertheless, we should acknowledge the contributions that the foreign private equity funds have played in various sectors of the economy in the post-crisis period. Foreign funds have invested in troubled Korean firms, understanding any risks involved, and successfully turned them around for the better. To that end, even if domestic private equity funds that have been set up since 2004 have not yet performed to the market expectation, we have to understand that they have further roles to play as we anticipate growth of the M&A market in the coming years.

Tools for Echelle Spectrograph of NYSC 1m Telescope

Wonseok Kang,Taewoo Kim,Jeongeun Kim,Yong Cheol Shin,Jihyun Yoo,Shinu Jeong,Yoonho Choi,Sun-gill Kwon 한국천문학회 2018 天文學會報 Vol.43 No.1

The Verification of Word-of-Mouth Communication Effect : With Focus on the Choice of College Students on Movie

Wonseok Kang,Jae-Hun Shin 경성대학교 산업개발연구소 2018 산업혁신연구 Vol.34 No.2

본 연구는 소비자의 영화 구매 의도에 구전의 각 차원이 어떤 차별적 영향을 미치는지 살펴보는 것을 주목적으로 하고, 구전의 각 차원인 구전 원천, 구전 방향성, 구전 정보 수용 시기가 차별적 구전효과를 갖는지 실증분석을 통해 검증 분석하고자 한다. 실증분석을 위해 구전 커뮤니케이션이 가장 활발하게 일어나는 대학생 그룹에 연구의 초점을 두었고 서울시에 거주하는 20대 초중반의 대학생을 대상으로 설문을 실시하였으며, 총 282개의 유효 설문을 표본으로 선정해 T-검정과 일원 분산분석을 실시하였다. 실증분석 결과, 구전 내용에 있어서는 영화의 내적 속성(내용, 재미, 감동)에 관한 구전을 들었을 때가 영화의 외적 속성(연출, 연기력, 배우 매력)에 관한 구전을 들었을 때보다 구전효과가 더 크다는 것이 입증되었는데, 이는 단순히 기분전환을 목적으로 하는 소비자의 영화관람 의도가 영화의 내적 속성에 더 가까운 것으로 해석되었으며, 개봉 전에 듣는 구전보다 개봉 후에 듣는 구전효과가 더 크다는 것이 입증되었는데, 개봉 후에 해당 영화에 관련된 정보의 빈도수가 더 높아지고 신빙성도 더 높아지기 때문인 것으로 추정할 수 있다. 마지막으로 개봉 전에는 긍정 구전을 접했을 때가 부정 구전을 접한 경우보다 구전효과가 더 크다는 것이 입증되었는데, 이는 개봉 전에 소비자들의 기대 심리로 인해 부정적 구전보다 긍정적 구전에 더 영향을 많이 받기 때문이라고 추정할 수 있다. 구전 원천에 관한 가설과 개봉 후 구전 방향성에 관한 가설은 기각되었는데 그 이유는 다음과 같다. 첫째, 구전 원천에 있어서는 정보통신기술이 발달하면서 언제 어디서든 볼 수 있는 인터넷과 SNS를 통한 네티즌의 구전효과가 클 것으로 생각하였지만, 오히려 정보통신기술이 발달하면서 친구나 전문가 평점에 대해서도 접근성이 높아지면서 세 집단 모두에 강한 영향을 받고 있기 때문에 집단 간의 영화 구매 의도에 미치는 영향력에 큰 차이가 없었다. 둘째, 개봉 후에 실제 영화를 본 사람들이 늘어나게 되면서 부정 구전이 늘어나고 신뢰성을 얻으면서 부정 구전이 긍정 구전보다 더 큰 영향력을 미칠 것이라고 생각하였지만, 오히려 부정 구전이 많아지면서 희소한 긍정 구전이 더 큰 영향력을 미쳐 개봉 후에도 긍정 구전이 부정 구전보다 영화 구매 의도에 더 큰 영향력을 주기 때문이라고 볼 수 있다. 결론적으로 본 연구결과를 통해 내용, 집단, 시기, 방향성 등 각 차원에 있어서 구전효과가 높고 강하게 나타나는 대학생들에 대해 실무자들이 정확히 파악하고 인지하여 긍정 구전은 극대화하고 부정 구전은 극소화하는 마케팅 전략을 수립하는 데 도움이 되기를 기대한다. This study is to examine the differential effect of each dimension of word-of-mouth such as source, direction and time of accepting the information on the consumer’s purchasing intention for the movie. For the empirical analysis, the survey was performed for college students living in Seoul whose age are in their early to mid 20s. 282 valid surveys in total were selected to implement the T-test and ANOVA. As a result, for the content of word-of-mouth, the effect of word-of-mouth was higher when they encountered the internal property of movie (story, enjoyment, impressiveness) than the external property of movie (directing, acting ability, attractiveness of actor or actress). Considering the consumers’ intention for watching movie is to simply refresh themselves, it can be interpreted that their intentions were more related to the internal property of movie. Also, the effect of word-of-mouth was higher after the movie was released than before it was. Furthermore, the result showed that the effect of word-of-mouth was higher when they heard positive word-of-mouth rather than negative word-of-mouth before the release of movie. In conclusion, the result of study implied that the executives should plan the marketing strategy to minimize the negative word-of-mouth and maximize the positive word-of-mouth. It can be achieved by considering the character of college students who are strongly and highly affected by each dimension of word-of-mouth such as the content, group, time and direction.

Longitudinal Assessment of Entecavir-induced Viral Load Reduction on Regulatory T Cells in Patients with Chronic Hepatitis B Virus Infection

Wonseok Kang,Jun Yong Park,Young Jun Choi,Jiwon Lee,Seung Up Kim,Do Young Kim,Kwang-Hyub Han,Eui-Cheol Shin,Sang Hoon Ahn 한국간담췌외과학회 2014 한국간담췌외과학회 학술대회지 Vol.2014 No.4