A Novel Transcriptomic Biosignature for Tuberculosis Diagnosis, Treatment Monitoring and Outcome Prediction

( Nguyen Phuoc Long ),( Nguyen Ky Phat ),( Nguyen Thi Hai Yen ),( Seongoh Park ),( Yumi Park ),( Yong-soon Cho ),( Jae-gook Shin ) 대한결핵 및 호흡기학회 2021 대한결핵 및 호흡기학회 추계학술대회 초록집 Vol.129 No.-

Background Transcriptomic biomarkers have been demonstrated as a promising tool for accurate diagnosis and differential diagnosis of tuberculosis (TB). However, little is known about their potential in TB treatment monitoring and outcome prediction. Methods We carried out a comprehensive search for available transcriptomics data. The data was used for the discovery of genes that show significant responses during the treatment of TB. Genes with consistent downtrend alterations were determined. Potential candidates were then subjected to external validation. The potential of the biomarker candidates in TB diagnosis and active TB progression risk evaluation was also evaluated. Results The transcriptome of the TB patients was significantly changed during the treatment. There were 371 significantly expressed genes with the monotonic downtrend alteration in the time series comparison. Among these genes, 10 genes were found to be associated with the TB treatment outcome. The 10-gene signature reflected well the downtrend kinetics of TB patients during the course of treatment. It had potential in predicting cured TB patients, when employed as covariates in a logistic regression model. In addition, biomarker candidates clearly differentiated TB patients from non-TB patients and people with latent infection. Conclusions The 10-gene biosignature had potential in TB diagnosis, treatment monitoring, and outcome prediction.

High-Throughput Omics and Statistical Learning Integration for the Discovery and Validation of Novel Diagnostic Signatures in Colorectal Cancer

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>

Global ginseng research

Nguyen, Phuoc Long,Nguyen, Hoang Anh,Park, Jeong Hill The Korean Society of Ginseng 2020 인삼문화 Vol.2 No.-

지금까지 Web of Science의 core collection에 나타난 인삼 관련 연구논문의 수를 분석하였다. 인삼논문이 처음 나타난 1905년부터 2019년까지 전세계에서 총 8,090편의 SCI(E) 논문이 출판된 것으로 나타났다. 그중 최근 24년, 즉, 1996년부터 2019년까지의 논문이 7,385편이었다. 1980년 18편에 불과했던 인삼 논문이 1990년에는 53편, 2000년에는 97편, 2010년에는 369편, 2019년에는 678편으로 비약적으로 증가하였다. Web of Science의 core collection에 수재된 전체 학술논문에서 인삼 논문이 차지하는 비중도 1970년 0.0008%, 1980년 0.0044%, 1990년 0.101%, 2000년 0.0141%에서 2019년에는 0.0422%로 비약적으로 증가하였다. 지난 24년간 출판된 인삼 연구논문 중 원보(노트 포함)는 7,099편, 리뷰는 286편이었다. 총 78개국 3,286개 기관에서 연구가 이루어졌으며, 1,274개 학술잡지에 논문이 수재되었다. 전체 논문 중 중국에서 연구된 논문이 40.3%로 가장 높았고, 대한민국에서 연구된 논문이 34.7%로 한국과 중국의 연구가 전체의 75%를 차지하였다. 그 다음은 미국(6.0%), 일본(4.1%), 캐나다(2.9%) 순이었다. 2013년까지는 한국에서 연구된 논문이 가장 많았으나 2014년부터 중국에서 연구된 논문의 수가 더 많아졌다. 지난 24년간 인삼은 전세계에서 가장 많이 연구된 약용식물로 인삼 다음으로는 차(6,499편), 마늘(3,641편), 은행(2,590편), 생강(1,945편) 순이었다. We conducted a comprehensive analysis of research papers on ginseng to provide an overview of global ginseng research. The qualitative and quantitative interpretation was carried out using collected data of Panax species and six other herbal plants from the Web of Science^TM Core Collection. We summarized and classified them by country/territory and institutions based on the corresponding author's institution. The first ginseng paper appeared in 1905 and since then, 8,090 papers have been published until 2019. Among them 7,385 papers were published in recent 24 years from 1996 to 2019. It was 18 papers in 1980, 53 in 1990, 97 in 2000, 369 in 2010, and increased to 678 in 2019. Proportion of ginseng papers in total number of scientific papers were also greatly increased, namely, 0.0008% in 1970, 0.0044% in 1980, 0.101% in 1990, 0.0141% in 2000, and 0.0422% in 2019. 7,099 original research papers including notes and 286 review papers were published during last 24 years. Total 3,286 institutions in 78 countries and 1,274 journals contributed to the publication of ginseng papers. Korea was the leading country in ginseng papers up to 2013, however, China took over the top from 2014. Chinese institutions contributed 40.3% of total papers followed by Korea (34.7%), USA (6.0%), Japan (4.1%), and Canada (2.9%). Ginseng was the most studied medicinal plant during last 24 years followed by tea, garlic, ginkgo, and ginger whose number of papers were 6,499, 3,641, 2,590, and 1,945, respectively.

A systematic review on metabolomics-based diagnostic biomarker discovery and validation in pancreatic cancer

Long, Nguyen Phuoc,Yoon, Sang Jun,Anh, Nguyen Hoang,Nghi, Tran Diem,Lim, Dong Kyu,Hong, Yu Jin,Hong, Soon-Sun,Kwon, Sung Won Springer-Verlag 2018 METABOLOMICS Vol.14 No.8

Meta-analysis of Metabolic Features Enables Reliable Interpretation for Tuberculosis Molecular Profile

( Nguyen Phuoc Long ),( Da Young Heo ),( Seongoh Park ),( Jae-gook Shin ),( Dong Hyun Kim ),( Jee Youn Oh ) 대한결핵 및 호흡기학회 2021 대한결핵 및 호흡기학회 추계학술대회 초록집 Vol.129 No.-

Background Metabolic perturbation is a crucial feature of tuberculosis (TB). Untargeted metabolomics has been widely used in metabolic phenotyping of TB patients. However, the biological interpretation using untargeted metabolomics data remains limited due to the capacity of compound identification. Methods We conducted untargeted metabolomics using plasma samples in a Korean cohort containing 63 pulmonary TB patients and 50 controls. In addition, metabolic features were extracted from a Chinese cohort including 35 pulmonary TB patients and 35 controls. The data was utilized for a pathway-level meta-analysis to elucidate the molecular processes associated with altered metabolic features in TB. Results The metabolic profile of TB patients was significantly different compared to that of the controls. Partial least-squares discriminant analysis from these metabolic features revealed an excellent discriminatory performance. The metabolic features were enriched in various metabolic processes, which are relevant concerning the pathophysiological processes of TB. Notably, we found the alterations of proinflammatory lipid mediators and metabolic processes associated with the innate immune responses. In addition, vitamin A and vitamin D3 metabolism appeared to be changed in TB patients. Several amino acidrelated pathways were also aberrant. There were some biological processes of which their role in TB remains to be elucidated. Conclusions Meta-analysis of metabolic features enables a reliable interpretation of tuberculosis molecular profile. This method could provide a start point for subsequent investigations in biomarker discovery and mechanistic elucidation.

Lipidomics Analysis Reveals Perturbation of Lipids Upon Harmane Exposure in Caenorhabditis elegans

Bao Tan Nguyen,Nguyen Thi Hai Yen,Ninh Khac Thanh Tung,Jong Seong Kang,Nguyen Phuoc Long,Hyung Min Kim 한국분석과학회 2023 학술대회논문집 Vol.2023 No.5

Multi-platform metabolomics and a genetic approach support the authentication of agarwood produced by <i>Aquilaria crassna</i> and <i>Aquilaria malaccensis</i>

Nguyen, Huy Truong,Min, Jung-Eun,Long, Nguyen Phuoc,Thanh, Ma Chi,Le, Thi Hong Van,Lee, Jeongmi,Park, Jeong Hill,Kwon, Sung Won Elsevier 2017 Journal of pharmaceutical and biomedical analysis Vol.142 No.-

<P><B>Abstract</B></P> <P>Agarwood, the resinous heartwood produced by some <I>Aquilaria</I> species such as <I>Aquilaria crassna</I>, <I>Aquilaria malaccensis</I> and <I>Aquilaria sinensis</I>, has been traditionally and widely used in medicine, incenses and especially perfumes. However, up to now, the authentication of agarwood has been largely based on morphological characteristics, a method which is prone to errors and lacks reproducibility. Hence, in this study, we applied metabolomics and a genetic approach to the authentication of two common agarwood chips, those produced by <I>Aquilaria crassna</I> and <I>Aquilaria malaccensis</I>. Primary metabolites, secondary metabolites and DNA markers of agarwood were authenticated by <SUP>1</SUP>H NMR metabolomics, GC–MS metabolomics and DNA-based techniques, respectively. The results indicated that agarwood chips could be classified accurately by all the methods illustrated in this study. Additionally, the pros and cons of each method are also discussed. To the best of our knowledge, our research is the first study detailing all the differences in the primary and secondary metabolites, as well as the DNA markers between the agarwood produced by these two species.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Current examination of agarwood is mostly based on visual examination and thus prone to error. </LI> <LI> Multi-platforms metabolomics well distinguished two popular agarwood types. </LI> <LI> DNA markers also showed clear differences in genetic variation between two agarwood species. </LI> <LI> Metabolomics and genetic approach both well supported the authentication of agarwood. </LI> </UL> </P>

Steroidomics for the Prevention, Assessment, and Management of Cancers: A Systematic Review and Functional Analysis

민영진,Nguyen Hoang Anh,Nguyen Phuoc Long,김선조,윤상준,김형민,권성원 한국분석과학회 2021 학술대회논문집 Vol.2021 No.11

Steroidomics is one of the most powerful analytical technique to find steroid biomarker. Current work conducted a comprehensive systematic review on steroidomics application in clinical field, especially in cancer research. Importantly, we suggest potential pitfalls and recommendations for clinical research based on steroidomics. After thorough screening on literature databases, we retrieved 45 papers that are suitable for our inclusion criteria. They were mostly about cancer risk predication including cancer diagnosis, prognosis, and monitoring after therapeutic intervention. Among all kinds of cancer, prostate cancer was one of the most frequently studied cancer. Dehydroepiandrosterone, estradiol, and cortisol, which were most frequently reported, were altered in at least four different types of cancer. Moreover, estrogen and its metabolites had high correlation with gynecologic cancers. Through pathway enrichment analysis, we found that androgen and estrogen metabolism, steroidogenesis, and androstenedione metabtholism were remarkably affected in cancers. Our analysis revealed that estradiol, dehydroepiandrosterone, cortisol, and estrogen metabolites could act as oncosteroids. Crucial shortcomings of these studies, however, includes an existence of potential confounding factors, small sample sizes, cross-sectional designs, and misuse of statistics. Further well-designed studies are required to empower current findings.

Facial landmarks detection for evaluating facial paralysis using a modern active shape model

Hung Phuoc Truong,Quan Manh Le,Thinh Long Nguyen,Yong-Guk Kim 한국HCI학회 2018 한국HCI학회 학술대회 Vol.2018 No.1

Facial nerve palsy makes patients lose voluntary muscles movement typically at one side of the human face and then it makes them difficult to interact with people using natural facial expressions. Detection of such symptom and evaluation of how serious it is should be a big challenge for standard face models. We propose a new method by which facial landmarks of the palsy face can be detected and measure the degree of the symptom using Discriminative Bayesian Active Shape Model (DB-ASM). Each patient was asked to make a few facial actions, such as eye closing, E-action and O-action with his mouth. We use facial landmarks detection method in measuring displacement ratios reflecting the structure of regions of eyebrows, eyes and mouth, respectively. There are three steps for this: annotating face model, fitting facial landmarks and measuring symmetry indices on the face. The present dataset contains many videos collected from 14 patients and 6 healthy persons. Experimental result suggests that the model with DB-ASM is useful as a facial landmarks predictor for facial paralysis patients.

Triclosan induces metabolomics alteration and reveals cellular toxicity in Caenorhabditis elegans

김석원,김형민,Nguyen Phuoc Long,윤상준,Huy Truong Nguyen,권성원 한국분석과학회 2021 학술대회논문집 Vol.2021 No.5