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Long, Nguyen Phuoc,Park, Seongoh,Anh, Nguyen Hoang,Nghi, Tran Diem,Yoon, Sang Jun,Park, Jeong Hill,Lim, Johan,Kwon, Sung Won MDPI 2019 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.20 No.2
<P>The advancement of bioinformatics and machine learning has facilitated the discovery and validation of omics-based biomarkers. This study employed a novel approach combining multi-platform transcriptomics and cutting-edge algorithms to introduce novel signatures for accurate diagnosis of colorectal cancer (CRC). Different random forests (RF)-based feature selection methods including the area under the curve (AUC)-RF, Boruta, and Vita were used and the diagnostic performance of the proposed biosignatures was benchmarked using RF, logistic regression, naïve Bayes, and k-nearest neighbors models. All models showed satisfactory performance in which RF appeared to be the best. For instance, regarding the RF model, the following were observed: mean accuracy 0.998 (standard deviation (SD) < 0.003), mean specificity 0.999 (SD < 0.003), and mean sensitivity 0.998 (SD < 0.004). Moreover, proposed biomarker signatures were highly associated with multifaceted hallmarks in cancer. Some biomarkers were found to be enriched in epithelial cell signaling in <I>Helicobacter pylori</I> infection and inflammatory processes. The overexpression of <I>TGFBI</I> and <I>S100A2</I> was associated with poor disease-free survival while the down-regulation of <I>NR5A2</I>, <I>SLC4A4</I>, and <I>CD177</I> was linked to worse overall survival of the patients. In conclusion, novel transcriptome signatures to improve the diagnostic accuracy in CRC are introduced for further validations in various clinical settings.</P>
Q-ray view를 이용한 유구치의 숨은 인접면 우식증 탐지
정연욱,이효설,최형준,이제호,최병재,김성오,Jeong, Younwook,Lee, Hyoseol,Choi, Hyungjun,Lee, Jaeho,Choi, Byungjai,Kim, Seongoh 대한소아치과학회 2015 大韓小兒齒科學會誌 Vol.42 No.3
본 연구는 Q-ray view (All in one Bio, Seoul, Korea)가 변연융선이 파괴되지 않은 유구치의 인접면 우식증을 적절히 탐지해 낼 수 있는지 알아보고자 하였다. 두 명의 소아치과의사가 3-9세 사이의 어린이 32명(평균연령 $5.6{\pm}1.3$세)의 유구치 인접면 100개를 시진, Q-ray view, DIAGNOdent (KaVo, Biberach, Germany), 디지털 치근단 방사선사진 촬영으로 평가하였다. 각 검사법과 실제 치료 시 관찰된 인접면 우식증의 진행 정도를 비교하였을 때, 법랑질 우식증에 대한 kappa값은 시진, Q-ray view, DIAGNOdent, 디지털 치근단 방사선사진 촬영 순으로 0.15, 0.10, 0.25, 0.68이었으며, 상아질 우식증에 대한 kappa값은 0.34, 0.56, 0.44, 0.70이었다. Q-ray view는 상아질까지 진행된 유구치의 숨은 인접면 우식증을 탐지하는 데 도움을 줄 수 있는 유용하고 간편한 보조장비가 될 수 있을 것으로 기대된다. The purpose of this study was to evaluate the ability of Q-ray view (All-in-one Bio, Seoul, Korea) in detection of proximal caries in primary molars with sound marginal ridges. Thirty two children aged 3-9 years (average $5.6{\pm}1.3$ years old) were chosen, and two examiners evaluated 100 proximal surfaces of primary molars with sound marginal ridges. The teeth were examined with; (a) visual examination, (b) Q-ray view, (c) DIAGNOdent (KaVo, Biberach, Germany) and (d) digital periapical radiography. Kappa statistic was used to assess the agreement between each examination method and the degree of caries progression. The kappa values for enamel caries were 0.15 (visual examination), 0.10 (Q-ray view), 0.25 (DIAGNOdent) and 0.68 (digital periapical radiography). The kappa values for dentinal caries were 0.34 (visual examination), 0.56 (Q-ray view), 0.44 (DIAGNOdent) and 0.70 (digital periapical radiography). Although Q-ray view showed low diagnostic ability in detection of enamel caries, it was effective in detection of hidden proximal caries extended into dentin. Q-ray view would be a useful and simple device which could aid pediatric dentists in detection of hidden proximal caries in primary molars especially when examining uncooperative children or disabled persons.
A New Approach for Time-dependent Cancer Volatiles Profiling via Isotope-labeling
Kyongjin Moon,Dong-Kyu Lee,Euiyeon Na,Seongoh Park,Jeong Hill Park,Johan Lim,Sung Won Kwon 한국분석과학회 2021 학술대회논문집 Vol.2021 No.11
While extensive research has been done on cancer detection using volatile biomarkers, the intracellular biochemical processes for the origin of biomarkers have not been fully elucidated. These limitations interrupt practical application of volatile biomarkers. Therefore, we developed a metabolism tracking method utilizing isotope labeling and flux analysis to overcome this problem. This novel method allows us to track intracellular volatiles and clarify their association with cancer metabolism. In this study, the carbon isotope ratio of <SUP>13</SUP>C-labeled lung cancer cell was measured using NanoSIMS-based imaging. The kinetic modeling of time-dependent isotopic ratio deduced the duration of cancer cell reaching a steady state of metabolism, at which point all potential intracellular volatiles are completely replaced by isotopes. In addition, by measuring the enrichment of isotopes in volatiles, it was revealed that 2-pentadecanone is derived from the fatty acid synthesis starting from glucose. Moreover, it was confirmed that this metabolic pathway is upregulated in cancer cells such as colon cancer, breast cancer, and pancreatic cancer compared to normal cells. These results indicate that this new method will be an effective strategy for tracing the origin of cancer volatiles and understanding intracellular metabolic pathways.
<i>In Vitro</i> Tracking of Intracellular Metabolism-Derived Cancer Volatiles via Isotope Labeling
Lee, Dong-Kyu,Na, Euiyeon,Park, Seongoh,Park, Jeong Hill,Lim, Johan,Kwon, Sung Won American Chemical Society 2018 ACS central science Vol.4 No.8
<▼1><P/><P>Cancer detection relying on the release of volatile biomarkers has been extensively studied, but the individual biochemical processes of the cells from which biogenic volatiles originate have not been thoroughly elucidated to date. Inadequate determination of the metabolic origin of the volatile biomarkers has limited the progress of the scientific and practical applications of volatile biomarkers. To overcome the current limitations, we developed a metabolism tracking approach combining stable isotope labeling and flux analysis of volatiles to trace the intracellular metabolism-derived volatiles and to reveal their relation to cancer metabolic pathways. Specifically, after the <SUP>13</SUP>C labeling of lung cancer cell, the isotopic ratio of whole cellular carbon was measured by nanoscale secondary ion mass spectrometry-based imaging. The kinetic modeling with the time-dependent isotopic ratio determined the period during which cancer cells reach the metabolic steady state, at which time all of the potential volatiles derived from intracellular metabolism were fully enriched isotopically. By measuring the isotopic enrichment of volatiles at the end-stage of isotopic flux, we found that 2-pentadecanone appeared to be derived from the metabolic cascade starting from glucose to fatty acid synthesis. Furthermore, this biosynthetic pathway was determined to be distinct in cancer, as it was upregulated in colon, breast, and pancreatic cancer cells but not in normal cells. The investigation of the metabolic footprint of 2-pentadecanone demonstrates that our novel approach could be applied to trace the metabolic origin of biogenic volatile organic compounds. This analytical strategy represents a potential cutting-edge tool in elucidating the biochemical authenticity of cancer volatiles and further expanding our understanding of the metabolic network of airborne metabolites <I>in vitro</I>.</P></▼1><▼2><P>We developed a combined stable isotope labeling and flux analysis of volatiles to trace the biochemical origin of volatiles and reveal their relation to cancer-specific metabolism.</P></▼2>