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RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study
Jung, Kyuwhan,Koh, InSong,Kim, Jeong-Hyun,Cheong, Hyun Sub,Park, Taejin,Nam, So Hyun,Jung, Soo-Min,Sio, Cherry Ann,Kim, Su Yeong,Jung, Euiseok,Lee, Byoungkook,Kim, Hye-Rim,Shin, Eun,Jung, Sung-Eun,Cho The Korean Academy of Medical Sciences 2017 JOURNAL OF KOREAN MEDICAL SCIENCE Vol.32 No.5
<P>Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling better quantification of gene expression than microarrays with a lower background signal. A total of 10 transcriptomes from 5 pairs of NEC lesions and adjacent normal tissues obtained from preterm infants with NEC were analyzed. As a result, a total of 65 genes (57 down-regulated and 8 up-regulated) revealed significantly different expression levels in the NEC lesion compared to the adjacent normal region, based on a significance at fold change ≥ 1.5 and <I>P</I> ≤ 0.05. The most significant gene, <I>DPF3</I> (<I>P</I> < 0.001), has recently been reported to have differential expressions in colon segments. Our gene ontology analysis between NEC lesion and adjacent normal tissues showed that down-regulated genes were included in nervous system development with the most significance (<I>P</I> = 9.3 × 10<SUP>−7</SUP>; <I>P<SUB>corr</SUB></I> = 0.0003). In further pathway analysis using Pathway Express based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, genes involved in thyroid cancer and axon guidance were predicted to be associated with different expression (<I>P<SUB>corr</SUB></I> = 0.008 and 0.020, respectively). Although further replications using a larger sample size and functional evaluations are needed, our results suggest that altered gene expression and the genes' involved functional pathways and categories may provide insight into NEC development and aid in future research.</P>
Leptin Polymorphisms Associated with Carcass Traits of Meat in Korean Cattle
Cheong, Hyun Sub,Yoon, Du-Hak,Kim, Lyoung Hyo,Park, Byung Lae,Chung, Eui Ryong,Lee, Han Ju,Cheong, Il-Cheong,Oh, Sung-Jong,Shin, Hyoung Doo Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.11
Leptin has been investigated as a candidate gene for fat characteristics in beef cattle. Previously, we have reported 57 sequence variants discovered in Korean cattle (Bos Taurus coreanae). In this study, we examined the association between polymorphisms of leptin and carcass traits (cold carcass weight (CWT) and marbling score (Marb)) in Korean cattle. Among 57 polymorphisms, 11 common polymorphic sites were genotyped in our beef cattle (n = 437). Statistical analysis revealed that one single nucleotide polymorphism in coding exon (c.+411T>C (A137A)) showed a significant association with the yield trait, CWT. The C-bearing genotypes (CC or CT) of c.+411T>C (A137A) showed the higher CWT (p = 0.006). c.+150C>G (S50S) also showed a significant association with the quality trait, Marb (p = 0.01). Our findings suggest that polymorphisms in leptin might be one of the important genetic factors that influence carcass yield and quality in beef cattle, especially in CWT and Marb.
Association of <i>RANBP1</i> haplotype with smooth pursuit eye movement abnormality
Cheong, Hyun Sub,Park, Byung Lae,Kim, Eun Mi,Park, Chul Soo,Sohn, Jin‐,Wook,Kim, Bong‐,Jo,Kim, Jae Won,Kim, Ki‐,Hoon,Shin, Tae‐,Min,Choi, Ihn‐,Geun,Han, Sang‐,Woo,H Wiley Subscription Services, Inc., A Wiley Company 2011 American Journal of Medical Genetics Part B: Neuro Vol. No.
<P><B>Abstract</B></P><P>Schizophrenia is a multifactorial disorder and smooth pursuit eye movement (SPEM) disturbance is proposed as one of the most consistent neurophysiological endophenotype in schizophrenia. The aim of this study was to examine the genetic association of <I>RANBP1</I> polymorphisms with the risk of schizophrenia and with the risk of SPEM abnormality in schizophrenia patients in a Korean population. Two SNPs of <I>RANBP1</I> were genotyped by TaqMan assay. Their genetic effect of single/haplotype polymorphisms on the risk of schizophrenia and SPEM abnormality from 354 patients and 396 controls were performed using <I>χ</I><SUP>2</SUP> and multiple regression analyses. Although no <I>RANBP1</I> polymorphisms were associated with the risk of schizophrenia, a common haplotype, <I>RANBP1‐ht2</I> (<I>rs2238798G–rs175162T</I>), showed significant association with the risk of SPEM abnormality among schizophrenia patients after multiple correction (<I>P</I><SUP>corr</SUP> = 0.002–0.0003). The results of present study provide the evidence that <I>RANBP1</I> on 22q11.21 locus might be causally related to the SPEM abnormality rather than the development of schizophrenia. © 2010 Wiley‐Liss, Inc.</P>
Inhibitory Effects of Corni Fructus on Testosterone-induced Benign Prostatic Hyperplasia in Rats
Hyun Hwangbo,Eun Ok Choi,Kyung-Il Kim,Son-Ho Yoon,Jung-Sub Jung,No-Jin Park,Ji-Suk Jeong,Jin-Woo Jeong,Cheol Park,Su Hyun Hong,Jae-Hun Cheong,Yung Hyun Choi 한국식품영양과학회 2017 한국식품영양과학회 학술대회발표집 Vol.2016 No.10
Epigenetic modification of retinoic acid-treated human embryonic stem cells
( Hyun Sub Cheong ),( Han Chul Lee ),( Byung Lae Park ),( Hye Min Kim ),( Mi Jin Jang ),( Yong Mahn Han ),( Seun Young Kim ),( Yong Sung Kim ),( Hyoung Doo Shin ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2010 BMB Reports Vol.43 No.12
Epigenetic modification of the genome through DNA methylation is the key to maintaining the differentiated state of human embryonic stem cells (hESCs), and it must be reset during differentiation by retinoic acid (RA) treatment. A genome-wide methylation/gene expression assay was performed in order to identify epigenetic modifications of RA-treated hESCs. Between undifferentiated and RA-treated hESCs, 166 differentially methylated CpG sites and 2,013 differentially expressed genes were discovered. Combined analysis of methylation and expression data revealed that 19 genes (STAP2, VAMP8, C10orf26, WFIKKN1, ELF3, C1QTNF6, C10orf10, MRGPRF, ARSE, LSAMP, CENTD3, LDB2, POU5F1, GSPT2, THY1, ZNF574, MSX1, SCMH1, and RARB) were highly correlated with each other. The results provided in this study will facilitate future investigations into the interplay between DNA methylation and gene expression through further functional and biological studies. [BMB reports 2010; 43(12): 830-835]
Cheong, Hyun Sub,Yoon, Du-Hak,Kim, Lyoung Hyo,Park, Byung Lae,Lee, Hye Won,Namgoong, Sohg,Kim, Eun Mi,Chung, Eui Ryong,Cheong, Il-Cheong,Shin, Hyoung Doo Asian Australasian Association of Animal Productio 2008 Animal Bioscience Vol.21 No.3
The insulin-like growth factor binding protein 3 (IGFBP3) has been investigated as a candidate gene for growth promoting effects in beef cattle and a modulator of IGF bioactivity. Previously, we have reported twenty two sequence variants discovered in Korean native cattle (Hanwoo). In this study, we examined the association between gene-specific polymorphisms of IGFBP3 and cold carcass weight (CW) and marbling score (MS) among Korean native cattle. Among twenty two polymorphisms, four common polymorphic sites (-854G>C, -100G>A, +421G>T and +3863C>A) were genotyped in our beef cattle (n = 437). Statistical analysis revealed that one common polymorphism in the promoter region (-854G>C) showed putative associations with MS (p = 0.03). IGFBP3 variation/haplotype information analyzed in this study will provide valuable information into strategies for the production of a commercial line of beef cattle.
NT5C3 polymorphisms and outcome of first induction chemotherapy in acute myeloid leukemia
Cheong, Hyun Sub,Koh, Youngil,Ahn, Kwang-Sung,Lee, Chansu,Shin, Hyoung Doo,Yoon, Sung-Soo Wolters Kluwer Health | Lippincott Williams Wilkin 2014 PHARMACOGENETICS AND GENOMICS Vol.24 No.9
AIMS: The cytosolic 5&vprime;-nucleotidase-III (NT5C3) is involved in the metabolism of the nucleoside analog, cytosine arabinose (AraC), and the expression level of NT5C3 is correlated with sensitivity to AraC in acute myeloid leukemia (AML) patients. The current study examined whether the NT5C3 polymorphisms could affect chemotherapy outcomes in 103 Korean AML patients. METHODS: Forty-seven single nucleotide polymorphisms in NT5C3 were genotyped using the Illumina GoldenGate genotyping assay. The genetic effects of the polymorphisms on the outcome of chemotherapy were analyzed using &khgr; and logistic regression models. RESULTS: Although none of the NT5C3 polymorphisms was associated with a complete remission rate, a common single nucleotide polymorphism, rs3750117, showed a significant association with induction rate after the first course of chemotherapy (Pcorr=0.004 and odds ratio=11.28) in AML patients. In addition, NT5C3 expression levels were significantly increased in patients with risk allele homozygote. CONCLUSIONS: The data suggest that genotyping the NT5C3 polymorphism may have the potential to identify patients more likely to respond to AraC-based chemotherapy.
Screening of genetic variations of SLC15A2, SLC22A1, SLC22A2 and SLC22A6 genes.
Cheong, Hyun Sub,Kim, Hae Deun,Na, Han Sung,Kim, Ji On,Kim, Lyoung Hyo,Kim, Seung Hee,Bae, Joon Seol,Chung, Myeon Woo,Shin, Hyoung Doo Springer-Verlag 2011 Journal of human genetics Vol.56 No.9
<P>A growing list of membrane-spanning proteins involved in the transport of a large variety of drugs has been recognized and characterized to include peptide and organic anion/cation transporters. Given such an important role of transporter genes in drug disposition process, the role of single-nucleotide polymorphisms (SNPs) in such transporters as potential determinants of interindividual variability in drug disposition and pharmacological response has been investigated. To define the distribution of transporter gene SNPs across ethnic groups, we screened 450 DNAs in cohorts of 250 Korean, 50 Han Chinese, 50 Japanese, 50 African-American and 50 European-American ancestries for 64 SNPs in four transporter genes encoding proteins of the solute carrier family (SLC15A2, SLC22A1, SLC22A2 and SLC22A6). Of the 64 SNPs, 19 were core pharmacogenetic variants and 45 were HapMap tagging SNPs. Polymorphisms were genotyped using the golden gate genotyping assay. After genetic variability, haplotype structures and ethnic diversity were analyzed, we observed that the distributions of SNPs in a Korean population were similar to other Asian groups (Chinese and Japanese), and significantly different from African-American and European-American cohorts. Findings from this study would be valuable for further researches, including pharmacogenetic studies for drug responses.</P>
Putative association of <i>SMAPIL</i> polymorphisms with risk of aspirin intolerance in asthmatics
Yongha Kim, Jason,Kim, Jeong-Hyun,Park, Byng-Lae,Sub Cheong, Hyun,Sook Park, Jong,Soo Jang, An,Uh, Soo-Taek,Choi, Jae-Sung,Kim, Yong-Hoon,Kim, Mi-Kyeong,Choi, Inseon S.,Heon Cho, Sang,Whui Choi, Byoun Informa Healthcare 2010 The Journal of asthma Vol.47 No.9
<P><I>Background.</I> Aspirin-intolerant asthma (AIA), as a clinical syndrome caused by aspirin, is characterized by lung inflammation and reversible bronchoconstriction. Recently, the altered trafficking and diminished airway reactivity have been implicated in allergic airway remodeling. The stromal membrane-associated protein 1-like (SMAP1L) exerts common and distinct functions in vesicle trafficking including endocytosis. The disturbance of pulmonary surfactant synthesis has been elucidated to be associated with asthma experimentally. Moreover, in alveolar type II (ATII) cells that synthesize pulmonary surfactant, alterations of clathrin-dependent endocytosis cause disturbance at the surfactant function, suggesting that SMAP1L, which directly interacts with clathrin, could be associated with asthma and related phenotypes. <I>Objective.</I> To verify our hypothesis that <I>SMAP1L</I> could play a role in the development of AIA, this study investigated associations between single-nucleotide polymorphisms (SNPs) of the <I>SMAP1L</I> gene and AIA. <I>Methods.</I> We conducted an association study between 19 SNPs of the <I>SMAP1L</I> gene and AIA in a total of 592 Korean subjects including 163 AIA and 429 aspirin-tolerant asthma (ATA) patients. Associations between polymorphisms of <I>SMAP1L</I> and AIA were analyzed with sex, smoking status, atopy, and body mass index as covariates. <I>Results.</I> Logistic analyses revealed that three common polymorphisms, <I>rs2982510</I>, <I>rs2294752</I>, and <I>rs446738</I>, were putatively associated with the increased susceptibility to AIA (<I>p</I> = .003, <I>p</I><SUP>corr</SUP> = .004, OR = 0.24, 95% CI = 0.09-0.62 for <I>rs2982510</I> and <I>rs2294752</I>; <I>p</I> = .008, <I>p</I><SUP>corr</SUP> = .03, OR = 0.44, 95% CI = 0.24-0.80 for <I>rs446738</I>, in the recessive model). In addition, <I>rs2982510</I> and <I>rs2294752</I> were significantly associated with the fall of forced expiratory volume in 1 s (FEV<SUB>1</SUB>) by aspirin provocation (<I>p</I> = .001, <I>p</I><SUP>corr</SUP> = .04 in the recessive model for both SNPs). <I>Conclusions.</I> Our findings suggest that <I>SMAP1L</I> might be a susceptible gene to AIA, providing a new strategy for the control of aspirin intolerance.</P>