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Shin JG, Kim DY, Seo JM, Oh JT, Park KW, Kim HY, Park BL, Kim JH, Shin HD. Potential association of VAMP5 polymorphisms with total colonic aganglionosis in Hirschsprung disease. Neurogastroenterol Motil 2016; 28:1055-63. [PMID: 26970437 DOI: 10.1111/nmo.12807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/29/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital bowel disease caused by the absence of nerve cells in portions of the intestine. Our recent genome-wide association study has identified a variant (rs1254900) of vesicle-associated membrane protein 5 (VAMP5) as a potential risk locus for total colonic aganglionosis (TCA) in HSCR. In addition, VAMP5 is a member of the VAMP/synaptobrevin protein complex, which participates in nerve signal transduction by regulating the vesicular fusion of the neurotransmitter in synaptic transmission. METHODS A total of 11 single nucleotide polymorphisms (SNPs), including those in the functionally important coding region, were selected on the basis of linkage disequilibrium and genotyped in 187 HSCR patients and 283 unaffected controls by using a TaqMan assay. Logistic analysis was conducted to investigate the possible association between VAMP5 SNPs and the risk of HSCR. KEY RESULTS Genetic variants of VAMP5 showed increased association signals in the TCA subgroup of HSCR patients (minimum p = 9.69 × 10(-5) , OR = 3.93 at rs10206961) compared to other subgroups, even after Bonferroni correction (pcorr = 0.002). In haplotype analysis, three haplotypes (BL1_ht1, BL2_ht1, and BL2_ht2) were associated with the risk of TCA (minimum pcorr = 0.005). In additional combined analysis after imputation based on our previous GWAS, five SNPs still retained significant associations with the TCA subtype (minimum pcorr = 0.006 at rs10206961). CONCLUSIONS & INFERENCES Considering that differential genetic effects on the development of the enteric nervous system, our results suggest that VAMP5 may be associated with the TCA of HSCR. However, further replications and functional evaluations are required.
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Affiliation(s)
- J-G Shin
- Department of Life Science, Sogang University, Seoul, Korea
| | - D-Y Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-M Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J-T Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - K-W Park
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - H-Y Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - B L Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - J-H Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - H D Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
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Chang HS, Shin SW, Lee TH, Bae DJ, Park JS, Kim YH, Uh ST, Choi BW, Kim MK, Choi IS, Park BL, Shin HD, Park CS. Development of a genetic marker set to diagnose aspirin-exacerbated respiratory disease in a genome-wide association study. Pharmacogenomics J 2015; 15:316-21. [PMID: 25707394 DOI: 10.1038/tpj.2014.78] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/28/2014] [Accepted: 11/05/2014] [Indexed: 12/27/2022]
Abstract
We developed a genetic marker set of single nucleotide polymorphisms (SNPs) by summing risk scores of 14 SNPs showing a significant association with aspirin-exacerbated respiratory disease (AERD) from our previous 660 W genome-wide association data. The summed scores were higher in the AERD than in the aspirin-tolerant asthma (ATA) group (P=8.58 × 10(-37)), and were correlated with the percent decrease in forced expiratory volume in 1 s after aspirin challenge (r(2)=0.150, P=5.84 × 10(-30)). The area under the curve of the scores for AERD in the receiver operating characteristic curve was 0.821. The best cutoff value of the summed risk scores was 1.01328 (P=1.38 × 10(-32)). The sensitivity and specificity of the best scores were 64.7% and 85.0%, respectively, with 42.1% positive and 93.4% negative predictive values. The summed risk score may be used as a genetic marker with good discriminative power for distinguishing AERD from ATA.
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Affiliation(s)
- H S Chang
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan, Republic of Korea
| | - S W Shin
- Asthma Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - T H Lee
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan, Republic of Korea
| | - D J Bae
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan, Republic of Korea
| | - J S Park
- 1] Asthma Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea [2] Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Y H Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Republic of Korea
| | - S T Uh
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - B W Choi
- Department of Internal Medicine, Chung-Ang University Yongsan Hospital, Seoul, Republic of Korea
| | - M K Kim
- Division of Internal Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - I S Choi
- Department of Allergy, Chonnam National University, Gwangju, Republic of Korea
| | - B L Park
- Department of Genetic Epidemiology, SNP Genetics Incorporation, Seoul, Republic of Korea
| | - H D Shin
- 1] Department of Genetic Epidemiology, SNP Genetics Incorporation, Seoul, Republic of Korea [2] Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - C S Park
- 1] Asthma Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea [2] Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
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Park TJ, Kim HJ, Kim JH, Bae JS, Cheong HS, Park BL, Shin HD. Associations of CD6, TNFRSF1A and IRF8 polymorphisms with risk of inflammatory demyelinating diseases. Neuropathol Appl Neurobiol 2014; 39:519-30. [PMID: 22994200 DOI: 10.1111/j.1365-2990.2012.01304.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 09/18/2012] [Indexed: 11/29/2022]
Abstract
AIMS Multiple sclerosis (MS) and neuromyelitis optica (NMO) are inflammatory autoimmune diseases that affect the central nervous system. Several genome-wide and candidate gene studies have identified genetic polymorphisms associated with the risk of MS or NMO. In particular, two recently published studies of meta-analysis in European-origin populations have suggested associations of single-nucleotide polymorphisms (SNPs) in CD6, TNFRSF1A and IRF8 with MS. The aim of our study was to assess the associations between SNPs in these three genes and the risk of inflammatory demyelinating disease (IDD) including MS and NMO. To the best of our knowledge, this is the first time such a study has been performed in an Asian population. METHODS A total of 21 SNPs of CD6, TNFRSF1A and IRF8 were genotyped in 178 IDD cases (79 MS and 99 NMO patients) and 237 normal controls in a Korean population. RESULTS Logistic analyses revealed that one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577 and rs1800693, P = 0.01-0.03) were associated with NMO. However, there was no association of IRF8 polymorphisms with IDD, including MS and NMO. Using further information from the SNP Function Prediction website, two exonic splicing enhancers (ESEs), including the polymorphic site of rs767455, were predicted to be binding sites for splicing factors (SRp55, SF2/ASF2 and SF2/ASF1). CONCLUSION Although additional studies are needed, our findings could provide information regarding the genetic aetiology of IDD in the Korean population.
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Affiliation(s)
- T-J Park
- Department of Life Science, Sogang University, Seoul, Korea
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Kim JY, Kim JH, Bae JS, Park BL, Uh ST, Kim MK, Choi IS, Cho SH, Park CS, Shin HD. Lack of association between GTF2H4 genetic variants and AERD development and FEV1 decline by aspirin provocation. Int J Immunogenet 2012; 39:486-91. [PMID: 22524621 DOI: 10.1111/j.1744-313x.2012.01118.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aspirin-exacerbated respiratory disease (AERD) is prevalent in about 10% of asthma patients and is characterized by a severe decline in forced expiratory volume in 1-s (FEV(1) ), an important phenotype for total lung capacity, upon ingestion of aspirin. The general transcription factor IIH subunit 4 (GTF2H4) is positioned at 6p21.33, a part of the major histocompatibility complex (MHC) class II region that contains a number of genes that play an important role in the immune system. In addition, genetic variants in another general transcription factor IIH gene have revealed significant association with lung disease. To investigate whether GTF2H4 genetic variants could be a causative factor for AERD development and FEV(1) decline by aspirin provocation, five common single-nucleotide polymorphisms (SNPs) were genotyped in 93 patients with AERD and 96 aspirin-tolerant asthma (ATA) controls. As a result, when adjusted for age, gender, smoking status and atopy as covariates, the rs1264307 variant and two haplotypes showed nominal signals in the association with AERD (P = 0.02-0.04), but the significances disappeared after corrections for multiple testing (corrected P > 0.05). In further multiple regression analysis, no genetic variants of GTF2H4 showed significant associations with FEV(1) decline by aspirin provocation in asthmatics (P > 0.05). Despite the need for replications in larger cohorts, our preliminary findings suggest that GTF2H4 variants may not be associated with susceptibility to AERD and obstructive symptoms in asthmatics.
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Affiliation(s)
- J Y Kim
- Department of Life Science, Sogang University, Seoul, Korea
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Pasaje CFA, Bae JS, Park BL, Cheong HS, Jang AS, Uh ST, Kim MK, Kim JH, Park TJ, Lee JS, Kim Y, Park CS, Shin HD. A possible association between ZNRD1 and aspirin-induced airway bronchoconstriction in a Korean population. J Investig Allergol Clin Immunol 2012; 22:193-200. [PMID: 22697009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND The etiology of aspirin-exacerbated respiratory disease (AERD) has been attributed to the combination of environmental and genetic risk factors. Although widely investigated in various diseases associated with immune dysfunction, the human zinc ribbon domain containing 1 (ZNRD1) gene is thought to play a role in the pathogenesis of AERD by altering the mechanisms involved in disease development. METHODS We selected 6 single-nucleotide polymorphisms (SNPs) for genotyping from the International HapMap database in order to analyze the association between polymorphisms in ZNRD1 and AERD in a Korean asthma cohort. Genotyping was carried out using the TaqMan assay, and differences in genotype frequency distributions were analyzed using logistic regression models. RESULTS Nominal associations were found between ZNRD1 rs1150740 and risk ofAERD via codominant and dominant genetic inheritance (P=.03; odds ratio, 1.14 [1.14-10.16]). The same polymorphism was found to be significantly associated with a decrease in forced expiratory volume in the first second of expiration, an important diagnostic marker of AERD, even after multiple testing corrections (P=.006, P(corr)=.03 in codominant and dominant models). CONCLUSIONS These preliminary findings suggest a possible relationship between ZNRD1 and aspirin-induced respiratory dysfunctions in a Korean population and provide essential information on the etiology of AERD.
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Affiliation(s)
- C F A Pasaje
- Department of Life Science, Sogang University, Seoul, Republic of Korea
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Pasaje CF, Bae JS, Park BL, Cheong HS, Kim JH, Park TJ, Lee JS, Kim Y, Park CS, Kim BJ, Cha B, Kim JW, Choi WH, Shin TM, Choi IG, Hwang J, Shin HD, Woo SI. Neuregulin 3 does not confer risk for schizophrenia and smooth pursuit eye movement abnormality in a Korean population. Genes Brain Behav 2011; 10:828-33. [PMID: 21762460 DOI: 10.1111/j.1601-183x.2011.00722.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Located on chromosome 10q22-q23, the human neuregulin3 (NRG3) is considered to be a strong positional and functional candidate gene for schizophrenia pathogenesis. Several case-control studies examining the association of polymorphisms in NRG3 with schizophrenia and/or related traits such as delusion have been reported recently in cohorts of Han Chinese, Ashkenazi Jews, Australians and white Americans of Western European ancestry. Thus, this study aimed to comprehensively investigate the association of NRG3 genetic variations with the risk of schizophrenia and smooth pursuit eye movement (SPEM) abnormality in a Korean population. Using TaqMan assay, six single-nucleotide polymorphisms (SNPs) in the intronic region of NRG3 were genotyped and two major haplotypes were identified in 435 patients with schizophrenia as cases and 393 unrelated healthy individuals as controls. A total of 113 schizophrenia patients underwent an eye tracking task, and degree of SPEM abnormality was measured using the logarithmic values of the signal/noise (Ln S/N) ratio. Differences in frequency distributions were analyzed using logistic and regression models following various modes of genetic inheritance and controlling for age and sex as covariates. Subsequent analysis revealed that the frequency distributions of NRG3 polymorphisms and haplotypes were similar between schizophrenia patients and healthy controls of Korean ethnicity. Furthermore, no significant differences were observed between the genetic variants tested for SPEM abnormality. By elucidating a lack of association in a Korean population, findings from this study may contribute to the understanding of the genetic etiology focusing on the role of NRG3 in schizophrenia pathogenesis.
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Affiliation(s)
- C-F Pasaje
- Department of Life Science, Sogang University, Seoul, Republic of Korea
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Lee SH, Jang AS, Woo Park S, Park JS, Kim YK, Uh ST, Kim YH, Chung IY, Park BL, Shin HD, Park CS. Genetic effect of single-nucleotide polymorphisms in the PPARGC1B gene on airway hyperreactivity in asthmatic patients. Clin Exp Allergy 2011; 41:1533-44. [PMID: 21692888 DOI: 10.1111/j.1365-2222.2011.03801.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Peroxisome proliferator-activated receptor gamma coactivator 1 beta (PPARGC1B) is a co-activator for intracellular receptors such as the estrogen receptor, PPAR, and glucocorticoid receptor, which are involved in asthma development. OBJECTIVES Genetic association of single-nucleotide polymorphisms (SNPs) in the PPARGC1B gene with the risk of asthma and airway hyperreactivity (AHR) was investigated, as well as the functional effects of these SNPs on PPARGC1B gene and protein expression. METHODS Direct sequencing of DNA from 24 Korean was performed to identify PPARGC1B SNPs. Genotyping was done in 264 controls and 949 asthmatics using single-base extension methods. PPARGC1B mRNA levels were measured using real-time PCR methodology. Luciferase and electrophoretic mobility shift assays (EMSA) were performed to functionally analyse PPARGC1B SNPs on promoter. RESULTS Eighteen SNPs and one insertion/deletion polymorphism were identified, and seven SNPs were genotyped. No significant difference existed in the distribution of SNPs and haplotypes between the asthmatics and controls. However, the allele frequency of -427C>T and +102525G>A;R265Q showed a significant association with log-transformed PC(20) methacholine values in the asthmatics (P=0.005-0.0004). Real-time PCR demonstrated higher PPARGC1B mRNA levels in asthmatics having -427CC allele than in those having -427TT or CT alleles (P=0.048). The ratio of the mRNA expression for each PPARGC1B exon4-mRNA compared with the wild type was similar in peripheral blood mononuclear cells carrying the +102525G>A allele. Luciferase reporter assays revealed that -427C allele caused higher promoter activity than -427T allele. EMSA demonstrated that -427C allele exhibited stronger binding activity to a nuclear protein in 293T cells than did the -427T allele. CONCLUSIONS AND CLINICAL RELEVANCE Polymorphisms of -427C>T on the promoter and those of +102525G>A on exon 5 of the PPARGC1B gene may affect the development of AHR through the modulation of PPARGC1B gene products. The PPARGC1B genotypes may serve as genetic markers for AHR.
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Affiliation(s)
- S-H Lee
- Genome Research Center for Allergy and Respiratory disease, Soonchunhyang University Hospital, Wonmi-gu, Bucheon, Gyeonggi-do, Republic of Korea
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Cheong HS, Park SM, Kim MO, Park JS, Lee JY, Byun JY, Park BL, Shin HD, Park CS. Genome-wide methylation profile of nasal polyps: relation to aspirin hypersensitivity in asthmatics. Allergy 2011; 66:637-44. [PMID: 21121930 DOI: 10.1111/j.1398-9995.2010.02514.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND In addition to the dysregulation of arachidonic acid metabolism in aspirin-intolerant asthma (AIA), aspirin acetylsalicylic acid (ASA) exerts effects on inflammation and immunity; however, many of these effects are unknown. OBJECTIVE The aim of the study was to evaluate the methylation status of whole genome in blood and polyp tissues with and without aspirin hypersensitivity. METHODS Genome-wide DNA methylation levels in nasal polyps and peripheral blood cells were examined by microarray analysis using five subjects with AIA and four subjects with aspirin-tolerant asthma (ATA). RESULTS In the nasal polyps of the patients with AIA, hypermethylation was detected at 332 loci in 296 genes, while hypomethylation was detected at 158 loci in 141 genes. Gene ontologic and pathway enrichment analyses revealed that genes involved in lymphocyte proliferation, cell proliferation, leukocyte activation, cytokine biosynthesis, cytokine secretion, immune responses, inflammation, and immunoglobulin binding were hypomethylated, while genes involved in ectoderm development, hemostasis, wound healing, calcium ion binding, and oxidoreductase activity were hypermethylated. In the arachidonate pathway, PGDS, ALOX5AP, and LTB4R were hypomethylated, whereas PTGES was hypermethylated. CONCLUSION The nasal polyps of patients with AIA have characteristic methylation patterns affecting 337 genes. The genes and pathways identified in this study may be associated with the presence of aspirin hypersensitivity in asthmatics and are therefore attractive targets for future research.
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Affiliation(s)
- H S Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Gasan-dong, Geumcheon-Gu, Seoul, Korea
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Kim JH, Park BL, Cheong HS, Pasaje CFA, Bae JS, Park JS, Jang AS, Uh ST, Choi JS, Kim YH, Kim MK, Choi IS, Cho SH, Choi BW, Koh IS, Park CS, Shin HD. Variations in the STK10 gene and possible associations with aspirin-intolerant asthma in a Korean population. J Investig Allergol Clin Immunol 2011; 21:378-388. [PMID: 21905501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Lymphocyte-oriented kinase deficiency encoded by the serine/threonine kinase 10 (STK10) gene correlates with the intracellular adhesion molecule 1 (ICAM-1)/lymphocyte function associated antigen 1 (LFA-1) complex in aspirin hypersensitivity. This study investigated the association between single nucleotide polymorphisms (SNPs) of STK10 and aspirin-intolerant asthma (AIA). METHODS A total of 54 SNPs were genotyped in 163 AIA patients and 429 aspirin-tolerant asthma (ATA) controls. RESULTS Logistic regression revealed that a synonymous variant (rs2306961G>A) had the most significant association with AIA (P = .008 under the codominant model; P = .004 under the dominant model), suggesting that tissue-specific codon usage between Lys_TTT and Lys_CTT could play a role in regulating expression of STK10 in airway epithelium. Haplotype analysis revealed that 4 haplotypes, including STK10_BL4-ht1, which is unique to rs2306961G>A, were significantly associated with aspirin hypersensitivity in asthmatics (P < .05). CONCLUSIONS Although replications in independent cohorts and further functional evaluations are needed, our preliminary findings suggest that STK10 polymorphisms might be susceptible genetic markers of AIA and that gene expression could be mediated by tissue-specific codon usage.
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Affiliation(s)
- J H Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea
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Jung MH, Park BL, Lee BC, Ro Y, Park R, Shin HD, Bae JS, Kang TC, Choi IG. Association of CHRM2 polymorphisms with severity of alcohol dependence. Genes Brain Behav 2010; 10:253-6. [PMID: 21176104 DOI: 10.1111/j.1601-183x.2010.00663.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cholinergic muscarinic 2 receptor (CHRM2) gene has been considered a candidate gene for the alcohol dependence in that it might underpin certain risk factors for this condition. This study examined variations in the CHRM2 between the patients with alcohol dependence and population controls in Korean and explored the associations between CHRM2 polymorphisms and severity of symptoms in the patients with alcohol dependence. One hundred and fifty-five patients with alcohol dependence, defined by the Alcohol Use Disorders Identification Test (AUDIT) and the Alcohol Dependence Scale (ADS) to measure the severity of symptoms, and one hundred and ninety-five population controls were drawn in the study. Three single nucleotide polymorphisms (SNPs) of CHRM2 were genotyped using the TaqMan assay and analyzed with the severity of symptoms of alcohol dependence. We found that although SNP rs324650 showed marginal association with the risk of alcohol dependence (P = 0.03), the significance of the result was not sustained after multiple corrections. SNP rs1824024 was significantly associated with the AUDIT and ADS scores in patients (P = 0.005 and 0.003, respectively). These findings suggested that the muscarinic acetylcholine function might be related not with alcohol dependence itself but with the severity of alcohol dependence in Korean population.
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Affiliation(s)
- M H Jung
- Department of Neuropsychiatry, Hallym University, Hangang Sacred Heart Hospital, Seoul, Republic of Korea
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Kim YJ, Kim HY, Kim JS, Lee JH, Yoon JH, Kim CY, Park BL, Cheong HS, Bae JS, Kim S, Shin HD, Lee HS. Putative association of transforming growth factor-alpha polymorphisms with clearance of hepatitis B virus and occurrence of hepatocellular carcinoma in patients with chronic hepatitis B virus infection. J Viral Hepat 2010; 17:518-26. [PMID: 19780938 DOI: 10.1111/j.1365-2893.2009.01205.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Previous studies showed that several genetic polymorphisms might influence the clinical outcome of chronic hepatitis B virus (HBV) infection, including HBV clearance or development of hepatocellular carcinoma (HCC). The aim of this study was to determine whether polymorphisms of the transforming growth factor-alpha (TGF-alpha) gene are associated with clinical outcome of HBV infection. A total of 1096 Korean subjects having either present or past evidence of HBV infection were prospectively enrolled between January 2001 and August 2003. Among 16 genetic variants in TGFA gene, nine variants were genotyped using TaqMan assay and the genetic association with HBV clearance and HCC occurrence was analysed. Statistical analyses revealed that TGFA+103461T>C, TGFA+106151C>G and TGFA-ht2 were marginally associated with clearance of HBV infection. However, only TGFA-ht2 retained significance after multiple correction (OR = 0.39, P(corr) = 0.007 in recessive model). Although no variants were significant after multiple correction, TGFA+88344G>A and TGFA+103461T>C were weakly associated in recessive model in the analysis of HCC occurrence. In addition, Cox relative hazards model also revealed that TGFA+88344G>A was associated with onset age of HCC occurrence in subjects (RH = 1.46, P(corr) = 0.04). TGF-alpha polymorphisms might be an important factor in immunity, progression of inflammatory process and carcinogenesis, which explains the variable outcome of HBV infection at least in part. Further biological evidence is warranted in the future to support these suggestive associations.
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Affiliation(s)
- Y J Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Chongno Gu, Seoul, Korea
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Hwang JY, Kim SY, Lee SH, Kim GS, Go MJ, Kim SE, Kim HC, Shin HD, Park BL, Kim TH, Hong JM, Park EK, Kim HL, Lee JY, Koh JM. Association of TWIST1 gene polymorphisms with bone mineral density in postmenopausal women. Osteoporos Int 2010; 21:757-64. [PMID: 19597909 DOI: 10.1007/s00198-009-1009-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 06/12/2009] [Indexed: 12/23/2022]
Abstract
UNLABELLED A novel polymorphism (+1871A>G) in the 3' flanking region and haplotypes were significantly associated with reduced osteoporosis risk and enhanced bone mineral density (BMD). These results suggest that TWIST1 may be a useful genetic marker for osteoporosis. Our results provide preliminary evidence supporting an association of TWIST1 with osteoporosis in postmenopausal women. INTRODUCTION TWIST1, a basic helix-loop-helix (bHLH) transcription factor, has been implicated in cell lineage determination and differentiation. METHODS To address the genetic variations in the TWIST1 gene associated with osteoporosis, we investigated the potential involvement of three TWIST1 single-nucleotide polymorphisms (SNPs) in osteoporosis in 729 postmenopausal women. BMD was measured using dual-energy X-ray absorptiometry. RESULTS A novel polymorphism in the 3' flanking region (+1871A>G) was significantly associated with osteoporosis risk (p = 0.007-0.008) and also in multiple comparison (p = 0.02). Consistent with these results, haplotype analysis showed that Block1_ht2 had protective effects in the dominant and additive model (p = 0.006-0.007). Specifically, the +1871A>G polymorphism was overdominantly associated with higher BMD values of the femoral neck (p = 0.039). CONCLUSION These results suggest that TWIST1 may be a useful genetic marker for osteoporosis and may have a role on bone metabolism in humans. Our results provide preliminary evidence supporting an association of TWIST1 with osteoporosis in postmenopausal women.
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Affiliation(s)
- J-Y Hwang
- The Center for Genome Science, National Institute of Health, Seoul, Republic of Korea
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Kim TH, Chang HS, Park SM, Nam BY, Park JS, Rhim T, Park HS, Kim MK, Choi IS, Cho SH, Chung IY, Park BL, Park CS, Shin HD. Association of angiotensin I-converting enzyme gene polymorphisms with aspirin intolerance in asthmatics. Clin Exp Allergy 2008; 38:1727-37. [PMID: 18727619 DOI: 10.1111/j.1365-2222.2008.03082.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Aspirin-intolerant asthma (AIA) refers to the development of bronchoconstriction in asthmatic individuals following the ingestion of aspirin or other non-steroidal anti-inflammatory drugs (NSAIDs). Angiotensin I-converting enzyme (ACE), a membrane-bound peptidase present in the lung, plays a pivotal role in the metabolism of the endogenous peptides involved in the pathogenesis of asthma. METHODS We screened a Korean asthma cohort (581 asthmatics including 81 aspirin-intolerant asthmatics and 231 aspirin-tolerant asthmatics, and 181 normal controls) for four single nucleotide polymorphisms (SNPs; -262 A>T and -115 T>C in the 5'-flanking region and +5467 T>C [Pro450Pro] and+11860 A>G [Thr776Thr] in the coding region) and one ins/del (+21288 CT) in the ACE gene. RESULTS None of the SNPs or haplotypes showed any association with the development of asthma, but they were significantly associated with the risk of AIA. Logistic regression indicated that the frequency of the rare alleles of -262 A>T and -115 T>C was higher in subjects with AIA than in subjects with aspirin-tolerant asthma (ATA) (P=0.003-0.01, P( corr)=0.015-0.05). Subjects homozygous for the rare alleles of -262 A>T and -115 T>C showed a greater decline in forced expiratory volume in 1 s (FEV(1)) after aspirin provocation than those homozygous for the common alleles (P<0.05). A luciferase reporter assay indicated that ACE promoters containing the rare -262 A>T allele possessed lower activity than did those containing the common allele (P=0.009). In addition, ACE promoters bearing the rare -115 T>C allele had no luciferase activity. DNA-protein binding assays revealed a band containing the ACE promoter region (including -262 A) and a protein complex. CONCLUSION The -262 A>T polymorphism in the promoter of the ACE gene is associated with AIA, and the rare allele of -262 A>T may confer aspirin hypersensitivity via the down-regulation of ACE expression.
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Affiliation(s)
- T-H Kim
- Genome Research Center for Allergy and Respiratory Disease, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi-do, Korea
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Kwak SH, Cho YM, Moon MK, Kim JH, Park BL, Cheong HS, Shin HD, Jang HC, Kim SY, Lee HK, Park KS. Association of polymorphisms in the insulin-degrading enzyme gene with type 2 diabetes in the Korean population. Diabetes Res Clin Pract 2008; 79:284-90. [PMID: 17913278 DOI: 10.1016/j.diabres.2007.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 08/22/2007] [Indexed: 11/23/2022]
Abstract
Insulin-degrading enzyme (IDE) is a metalloproteinase which degrades insulin and terminates its action. Homologous deletion of IDE gene resulted in hyperinsulinemia and glucose intolerance in a rat model of type 2 diabetes mellitus. Several genetic association studies examined IDE as a susceptibility gene for type 2 diabetes in European descents. Here we investigated the genetic association of IDE polymorphisms with the risk of type 2 diabetes and its related phenotypes in the Korean population. Among six single nucleotide polymorphisms analyzed, g.-179T>C (OR=1.73, P=0.04), and g.IVS18+99G>A (OR=1.23, P=0.02) revealed borderline association with increased risk of type 2 diabetes. Combining our results with previous data obtained from the European population, g.-179T>C (OR=1.11, P=0.03), and g.IVS24-64A>T (OR=1.18, P=0.005) showed significant association with type 2 diabetes. Haplotype consisting of common alleles of the six polymorphisms was associated with decreased risk of type 2 diabetes (OR=0.82, P=0.02). However, none of the polymorphisms was significantly associated with metabolic phenotypes. We can conclude that variations in IDE might contribute to diabetes susceptibility in the Korean population.
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Affiliation(s)
- S H Kwak
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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15
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Kim Y, Park CS, Shin HD, Choi JW, Cheong HS, Park BL, Choi YH, Jang AS, Park SW, Lee YM, Lee EJ, Park SG, Lee JY, Lee JK, Han BG, Oh B, Kimm K. A promoter nucleotide variant of the dendritic cell-specific DCNP1 associates with serum IgE levels specific for dust mite allergens among the Korean asthmatics. Genes Immun 2007; 8:369-78. [PMID: 17460725 DOI: 10.1038/sj.gene.6364394] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Dendritic cells (DCs), the most abundant antigen-presenting cells in the lung, have been drawing attention for their roles in specific allergic responses to aeroallergens with support of Th lymphocytes, and in persistent inflammatory changes in allergic asthma. To identify genetic factors that may be involved in the asthma susceptibility and development of the disease phenotypes, we examined association of DC-specific DCNP1 polymorphisms with the disease risk. The case-control study revealed association of the nucleotide variants with serum immunoglobulin E (IgE) levels specific for Dermatophagoides farinae (Der f 1) and Dermatophagoides pteronyssinus (Der p 1), major aeroallergens of dust mites, among subjects with asthma. In particular, the T-allele-carrying genotype frequencies for one of the variants (c.-1289C>T) located in the promoter region were found increased in the asthmatic group with low levels of the mite-specific IgE (odds ratio (OR)=0.63 (0.48-0.83) for Der p 1). Results from functional analyses indicated that the promoter variant would affect the gene expression by modulating DNA-protein interaction. We propose that the genetic polymorphism of DCNP1 may influence production of specific IgE by altering DC functions in the mite allergen presenting and/or processing. The functional relevance of the genetic variation would provide an important insight into the genetic basis of allergic response to the mite antigens.
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Affiliation(s)
- Y Kim
- The Center for Genome Science, National Institute of Health, Eunpyung-Gu, Seoul, Korea.
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Cheong HS, Yoon D, Kim LH, Park BL, Lee HW, Han CS, Kim EM, Cho H, Chung ER, Cheong I, Shin HD. Titin-cap (TCAP) polymorphisms associated with marbling score of beef. Meat Sci 2007; 77:257-63. [PMID: 22061598 DOI: 10.1016/j.meatsci.2007.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 03/13/2007] [Accepted: 03/14/2007] [Indexed: 10/23/2022]
Abstract
Marbling score (MS) is the major qualitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the titin-cap gene (TCAP) and carcass traits in Korean native cattle (also known as Hanwoo). By direct DNA sequencing in 24 unrelated Korean cattle, we identified five sequence variants in 1.2kb of TCAP. Among them, four common polymorphic sites were selected for genotyping in the beef cattle (n=437). Pair-wise linkage analysis with four polymorphisms showed strong linkage disequilibrium (LD), and three major haplotypes (freq.>0.1) were constructed. Statistical analysis revealed that polymorphisms in intron1 (g.346G>A) and exon2 (g.592-597CTGCAG[Leu-Gln]insdel) showed significant association with marbling score (P(cor.)=0.003 and 0.02, respectively). One haplotype, ht2[C-G-G-del], also showed significant association with MS (P(cor.)=0.0004). Our findings suggest that polymorphisms in TCAP might be among the important genetic factors involved in carcass quality in beef cattle.
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Affiliation(s)
- H S Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Rm 1407, Complex B, WooLim Lion's Valley, 371-28, Gasan-Dong, Geumcheon-Gu, Seoul, 153-803, Republic of Korea
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17
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Koh JM, Park BL, Kim DJ, Kim GS, Cheong HS, Kim TH, Hong JM, Shin HI, Park EK, Kim SY, Shin HD. Identification of novel RANK polymorphisms and their putative association with low BMD among postmenopausal women. Osteoporos Int 2007; 18:323-31. [PMID: 17115234 DOI: 10.1007/s00198-006-0244-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Accepted: 09/25/2006] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Bone mineral density (BMD) is the major factor for determining bone strength, which is closely correlated to osteoporotic fracture risk and is largely determined by multiple genetic factors. The RANK (TNFRSF11A), receptor for RANKL, is a member of the tumor necrosis factor receptor (TNFR) superfamily and plays a central role in osteoclast development. METHODS In order to investigate the effects of RANK polymorphism on BMD and osteoporosis, we directly sequenced the RANK gene in 24 Korean individuals and identified 25 sequence variants. Eleven of these polymorphisms were selected and genotyped in a larger-scale study of postmenopausal women (n = 560). Areal BMD (g/cm(2)) of the anterior-posterior lumbar spine and the nondominant proximal femur were measured using dual-energy X-ray absorptiometry. RESULTS We found that two intronic polymorphisms in the RANK gene [RANK + 34863G > A (rs12458117) and RANK + 35928insdelC (new polymorphism found in this study) in intron 6] were significantly associated with the BMD of the lumbar spine, i.e., rare alleles were significantly associated with low BMD of the lumbar spine among Korean postmenopausal women (p = 0.04 and 0.02, respectively). These polymorphisms were also associated with low BMD of proximal femur sites, including Ward's triangle, trochanter, and total femur. Our results suggest that +34863G > A and +35928insdelC polymorphisms in RANK are possible genetic factors for low BMD in postmenopausal women.
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Affiliation(s)
- J-M Koh
- Division of Endocrinology and Metabolism, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 138-736, South Korea
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Koo BK, Cho YM, Park BL, Cheong HS, Shin HD, Jang HC, Kim SY, Lee HK, Park KS. Polymorphisms of KCNJ11 (Kir6.2 gene) are associated with Type 2 diabetes and hypertension in the Korean population. Diabet Med 2007; 24:178-86. [PMID: 17257281 DOI: 10.1111/j.1464-5491.2006.02050.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS Kir6.2 is found in the pancreatic B-cell, cardiac and skeletal muscle and non-vascular smooth muscle. KCNJ11, encoding Kir6.2, has been shown to be associated with both Type 2 diabetes mellitus and cardiovascular disease in several populations. In this study, we investigated whether polymorphisms in KCNJ11 are associated with Type 2 diabetes and other metabolic phenotypes in the Korean population. METHODS We sequenced KCNJ11 to identify common polymorphisms using 24 Korean DNA samples. Of the 14 polymorphisms found in KCNJ11, six common ones [genomic sequence (g.)-1709A>T, g.-1525T>C, g.67G>A (E23K), g.570C>T (A190A), g.1009A>G (I337V), and g.1388C>T] were genotyped in 761 Type 2 diabetic patients and in 630 non-diabetic subjects. RESULTS All the polymorphic loci in KCNJ11 are in strong linkage disequilibrium in the Korean population and act as one haplotype block. g.67G>A and g.1009A>G were associated with an increased risk of Type 2 diabetes [age, sex, and body mass index (BMI)-adjusted odds ratios (OR) = 1.376 (1.085-1.745), P = 0.008 and 1.411 (1.111-1.791), P = 0.005, respectively], as was one haplotype (A-T-A-C-G-C in the order of polymorphisms as shown above) containing g.67A and g.1009G [OR = 1.359 (1.080-1.709), P = 0.009]. The haplotype (A-T-A-C-G-C) was also strongly associated with hypertension [OR = 1.655 (1.288-2.126), P < 0.001]. CONCLUSIONS Polymorphisms in KCNJ11 are associated with Type 2 diabetes and also with hypertension in the Korean population.
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Affiliation(s)
- B K Koo
- Department of Internal Medicine, Seoul National University College of Medicine, Chongno-Gu, Seoul, Korea
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Park KS, Shin HD, Park BL, Cheong HS, Cho YM, Lee HK, Lee JY, Lee JK, Kim HT, Park CS, Han BG, Kimm K, Oh B. Putative association of peroxisome proliferator-activated receptor gamma co-activator 1beta (PPARGC1B) polymorphism with Type 2 diabetes mellitus. Diabet Med 2006; 23:635-42. [PMID: 16759305 DOI: 10.1111/j.1464-5491.2006.01882.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Peroxisome proliferator-activated receptor gamma co-activator 1beta (PPARGC1B) may play an important role in obesity and Type 2 diabetes mellitus (T2DM). In an effort to identify genetic polymorphisms in potential candidate genes for T2DM, genetic associations of PPARGC1B were examined in a Korean T2DM study. METHODS We have sequenced the PPARGC1B, and examined its association with T2DM and diabetic phenotypes in a Korean T2DM study (775 T2DM patients and 316 control subjects) using the TaqMan method. Logistic and multiple regression models were employed to analyse the genetic contributions of polymorphisms. Nineteen polymorphisms were identified in PPARGC1B. RESULTS By logistic regression analysis controlling for age and sex as covariates, one non-synonymous single-nucleotide polymorphism (SNP; +102605C>A; Arg292Ser) in exon 5 showed marginal significant associations with the risk of T2DM. The allele frequency of the minor allele ['A (= Ser)' allele of +102605C>A] was lower among T2DM patients (frequency = 0.101) than among control subjects (frequency = 0.135) [P = 0.03, OR = 0.71 (95% CI: 0.51-0.94)]. Furthermore, serum triglyceride level was also associated with this non-synonymous SNP (+102605C>A; Arg292Ser) in exon 5 among controls (P = 0.03 in the dominant analysing model). Serum triglyceride levels [1.46 +/- 0.70 (log-transformed value; 0.12 +/- 0.18)] were lower in individuals who carry one or two copies of minor alleles than among others [1.60 +/- 0.85 (log-transformed value; 0.16 +/- 0.21)]. CONCLUSION The present study provides, for the first time, information about genetic polymorphisms in PPARGC1B and putative associations of one non-synonymous SNP with the risk of T2DM and serum triglyceride (TG) levels in the Korean population, although this result was not significant after correction for multiple testing.
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Affiliation(s)
- K S Park
- Genome Research Center for Diabetes and Endocrine Disease, Clinical Research Institute, Seoul National University Hospital, Korea
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Hur JW, Sung YK, Shin HD, Park BL, Cheong HS, Bae SC. Poly(ADP-ribose) polymerase (PARP) polymorphisms associated with nephritis and arthritis in systemic lupus erythematosus. Rheumatology (Oxford) 2006; 45:711-7. [PMID: 16461442 DOI: 10.1093/rheumatology/kei262] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE The objective of this study was to confirm whether polymorphisms of the poly(ADP-ribose) polymerase gene (PARP) are associated with genetic susceptibility to systemic lupus erythematosus (SLE) and to investigate the possible association of nephritis and arthritis in SLE with PARP polymorphisms. METHODS Using direct DNA sequencing in 24 individuals, we identified 44 sequence variants within exons and their flanking regions, including the 1.5-kb promoter region of PARP. Six common polymorphic sites were selected for larger-scale genotyping (in 350 Korean SLE patients and 330 healthy controls), which identified six common haplotypes. RESULTS Although no statistically significant association with the risk of SLE was observed, we found that two single-nucleotide polymorphisms (SNPs -1963A --> G and +28077G --> A) were significantly associated with an increased risk of nephritis, and one non-synonymous variant [+40329T --> C(V762A)] was also significantly associated with an increased risk of arthritis, while the -1963A --> G SNP showed a protective effect on arthritis in Korean SLE patients. CONCLUSION Our results demonstrate that PARP polymorphisms are not associated with SLE susceptibility, but that -1963A --> G, +28077G --> A and +40329T --> C(V762A) are significantly associated with nephritis and arthritis in Korean SLE patients.
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Affiliation(s)
- J-W Hur
- Department of Internal Medicine, Hospital for Rheumatic Diseases, Hanyang University, Seoul, Republic of Korea
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Hwang JY, Lee JY, Park MH, Kim KS, Kim KK, Ryu HJ, Lee JK, Han BG, Kim JW, Oh B, Kimm K, Park BL, Shin HD, Kim TH, Hong JM, Park EK, Kim DJ, Koh JM, Kim GS, Kim SY. Association of PLXNA2 polymorphisms with vertebral fracture risk and bone mineral density in postmenopausal Korean population. Osteoporos Int 2006; 17:1592-601. [PMID: 16932874 DOI: 10.1007/s00198-006-0126-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2006] [Accepted: 03/20/2006] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Plexin A2 (PLXNA2) is a receptor that recognizes secreted or membrane-bound semaphorin 3A, which is implicated in neural regulation of bone metabolism. MATERIALS AND METHODS In the present study, we identified 48 genetic polymorphisms in PLXNA2 by resequencing, and 10 single nucleotide polymorphisms (SNPs) were selected for further investigation into their potential involvement in osteoporosis in a postmenopausal population (n=560). RESULTS Two SNPs, +14G>A (Gln5Arg) and +183429C>T (Tyr1621Tyr), and Block1-ht2 were associated with risk of vertebral fracture (p=0.01-0.05), and three SNPs, +799G>A (Ala267Thr), +135391G>A, and +190531G>C, were associated with bone mineral density at various femur sites (p=0.003-0.03). Particularly, the minor allele of +14G>A was associated with a protective effect on vertebral fracture and higher lumbar bone mineral density, suggesting that +14G>A may be a useful marker for osteoporosis and its related fracture. CONCLUSION These results provide, for the first time, evidence supporting the association of PLXNA2 with osteoporosis in postmenopausal women.
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Affiliation(s)
- J-Y Hwang
- National Genome Research Institute, National Institute of Health, 5 Nokbun-dong, Eunpyung-gu, Seoul, 122-701, South Korea
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Shin HD, Park KS, Park BL, Cheong HS, Cho YM, Lee HK, Lee JY, Lee JK, Kim HT, Han BG, Kim JW, Koh I, Kim YJ, Oh B, Kimm K, Park C. Common promoter polymorphism in monocyte differentiation antigen CD14 is associated with serum triglyceride levels and body mass index in non-diabetic individuals. Diabet Med 2006; 23:72-6. [PMID: 16409569 DOI: 10.1111/j.1464-5491.2005.01732.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
AIMS Growing evidence supports the hypothesis that chronic low-grade inflammation related to innate immunity may play an important role in the pathophysiology of Type 2 diabetes mellitus (T2DM). The monocyte differentiation antigen CD14 gene (CD14) acts as the receptor for lipopolysaccharide (LPS) and augments monocyte/macrophage inflammatory responses. METHODS We have sequenced the gene, including all exons, exon/intron boundaries, and the -1.5 kb of the 5' flanking region. Two common loci (minor allele frequency > 0.05) were genotyped in 775 T2DM patients and 316 control subjects recruited in the Korean T2DM Study. RESULTS Eight polymorphisms, including four non-synonymous forms, were identified in CD14. No polymorphisms were found in association with T2DM. However, one common promoter SNP (-260T>C) was significantly associated with both the serum triglyceride level (TG) and body mass index (BMI) in non-diabetic control subjects. Individuals who carried the minor allele (C) had higher TG levels (1.65 +/- 0.81 vs. 1.46 +/- 0.80 mmol/l; P = 0.0007) and BMI (23.96 +/- 3.00 vs. 23.28 +/- 3.22 kg/m(2); P = 0.04) as compared with subjects carrying T/T genotypes. CONCLUSION Our data suggest that lipid metabolism and obesity, important pathophysiological elements of T2DM and the metabolic syndrome, are regulated by complex mechanisms that include the CD14 gene polymorphism-mediated genetic propensity to non-specific inflammatory responses.
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Affiliation(s)
- H D Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
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Sung YK, Park BL, Shin HD, Kim LH, Kim SY, Bae SC. Interleukin-10 gene polymorphisms are associated with the SLICC/ACR Damage Index in systemic lupus erythematosus. Rheumatology (Oxford) 2005; 45:400-4. [PMID: 16287924 DOI: 10.1093/rheumatology/kei184] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Overproduction of interleukin-10 (IL-10) is a pivotal feature in the pathophysiology of systemic lupus erythematosus (SLE). We examined the IL10 genotype of Korean patients with SLE and normal controls to determine whether associations exist between the pattern of inherited IL10 genes and SLE susceptibility or the SLICC/ACR Damage Index (SDI). METHODS A total of 350 Korean SLE patients and 330 healthy subjects were enrolled. Direct DNA sequencing and primer extension procedures were employed. Logistic regression analyses were performed to examine the genetic association with SLE and SDI. RESULTS Eight sequence variants were identified by direct DNA sequencing in 24 Korean individuals. Five of the polymorphisms were selected for larger scale genotyping (n = 680) by considering their allele frequencies, haplotype-tagging status and linkage disequilibrium coefficients among polymorphisms. Haplotypes and allele distributions of the IL10 polymorphisms did not differ significantly between SLE patients and controls. Among identified SNPs, the rare C allele of IL10-592A-->C was significantly associated with the SDI among SLE patients in the following three alternative models: codominant (P = 0.007, odds ratio = 1.70), dominant (P = 0.02, odds ratio = 1.85) and recessive (P = 0.05, odds ratio = 2.25). Similarly, IL10+955T-->G and IL10-ht2 were significantly associated with the SDI in the codominant and dominant models. CONCLUSION IL10 polymorphisms are not associated with disease susceptibility in Korean patients with SLE. However, IL10-592A-->C, IL10+955T-->G and IL10-ht2 are significantly associated with the SDI, suggesting that IL10-592C, IL10+955G and IL10-ht2 accelerate the damage induced by SLE.
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Affiliation(s)
- Y-K Sung
- Department of Internal Medicine, Division of Rheumatology, Hanyang University, Seongdong-Gu, Seoul 133-792, South Korea
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Shin HD, Park BL, Kim LH, Cheong HS, Kim JH, Cho YM, Lee HK, Park KS. Association of a polymorphism in the gene encoding phosphoenolpyruvate carboxykinase 1 with high-density lipoprotein and triglyceride levels. Diabetologia 2005; 48:2025-32. [PMID: 16132948 DOI: 10.1007/s00125-005-1917-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Accepted: 05/16/2005] [Indexed: 10/25/2022]
Abstract
AIMS/HYPOTHESIS Phosphoenolpyruvate carboxykinase (PCK) is the key enzyme involved in the regulation of gluconeogenesis. The aim of this study was to identify genetic polymorphisms in potential candidate genes for type 2 diabetes by sequencing all exons in the PCK genes (PCK1 and PCK2), and examining the association with type 2 diabetes and diabetic phenotypes in a Korean population (775 type 2 diabetic patients and 316 normal control subjects). MATERIALS AND METHODS Twenty-two polymorphisms in PCK1 and PCK2 were identified in a Korean population (n=24) by direct DNA sequencing. The TaqMan genotyping method was applied for genotyping the remainder of the study population. Associations of PCK polymorphisms with the risk of type 2 diabetes and diabetic phenotypes were analysed using logistic and multiple regressions, adjusting for age, sex and BMI. RESULTS Although no significant associations between the genetic polymorphisms in PCK genes and the risk of type 2 diabetes were detected, in further haplotype analysis, one of the common haplotypes, PCK1 ht3, revealed susceptibility to type 2 diabetes (p=0.006). One 3' untranslated region (UTR) single nucleotide polymorphism (SNP) also showed an association with HDL levels among non-diabetic control subjects: individuals homozygous for the major allele (T/T) had the lowest HDL level (1.11+/-0.32 mmol/l), heterozygotes (T/C) had an intermediate level (1.27+/-0.37 mmol/l), and those homozygous for the minor allele (C/C) had the highest level (1.39+/-0.28 mmol/l) (p=0.000003). This 3' UTR SNP was also associated with triglyceride levels, with a lower triglyceride level observed among individuals who were homozygous for the minor allele (C/C) than among those who were not. CONCLUSIONS/INTERPRETATION The strong genetic association of HDL and triglyceride levels with variation/haplotype information identified in this study would be useful for further genetic epidemiological studies of this important gene.
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Affiliation(s)
- H D Shin
- Department of Genetic Epidemiology, SNP Genetics, Seoul, Korea
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Cho YM, Shin HD, Park BL, Kim JH, Park KS, Kim SY, Lee HK. Association between polymorphisms in the nuclear respiratory factor 1 gene and type 2 diabetes mellitus in the Korean population. Diabetologia 2005; 48:2033-8. [PMID: 16082529 DOI: 10.1007/s00125-005-1855-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Accepted: 04/02/2005] [Indexed: 01/07/2023]
Abstract
AIMS/HYPOTHESIS Dysfunction in mitochondrial oxidative phosphorylation plays a central role in insulin resistance and type 2 diabetes. Nuclear respiratory factor 1 (NRF1) is a transcription factor that acts on nuclear genes encoding respiratory subunits and components of the mitochondrial transcription and replication machinery. Thus, we investigated its genetic association with type 2 diabetes. METHODS The NRF1 gene was sequenced to identify polymorphisms in 24 Korean DNA samples and then common variants were genotyped in 766 patients with type 2 diabetes and 303 non-diabetic subjects. RESULTS Twelve single nucleotide polymorphisms and one insertion/deletion polymorphism were identified. Six common variants among them were genotyped in a larger study. Although three individual polymorphisms appeared to be associated with type 2 diabetes (g.-46350insdel A, g.+141G>T and g.+54529A>G), the effects were only marginal. However, a haplotype (H2) was associated with a decreased risk of type 2 diabetes and another haplotype (H4) was associated with an increased risk of type 2 diabetes (p values for the Haplo. Score test were 0.009 and 0.004, respectively). CONCLUSIONS/INTERPRETATION We demonstrated that two common haplotypes of NRF1 gene are associated with type 2 diabetes in the Korean population.
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Affiliation(s)
- Y M Cho
- Department of Internal Medicine, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul 110-744, South Korea
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Hur JW, Shin HD, Park BL, Kim LH, Kim SY, Bae SC. Association study of Toll-like receptor 9 gene polymorphism in Korean patients with systemic lupus erythematosus. ACTA ACUST UNITED AC 2005; 65:266-70. [PMID: 15730519 DOI: 10.1111/j.1399-0039.2005.00374.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mammalian Toll-like receptors (TLR) play an important role in both adaptive immunity and innate immunity. Genetic variations within TLR genes are known to be associated with a variety of inflammatory and infectious diseases. TLR9 is potentially associated with autoimmune diseases, because it participates in the production of pro-inflammatory cytokines and the maturation of dendritic cells. We investigated the association of four TLR9 gene polymorphisms (-1486 T>C, -1237 C>T, +1174 A>G and +2848 G>A) with the susceptibility to systemic lupus erythematosus (SLE) and related phenotypes in 680 Korean people (350 SLE patients and 330 controls). TLR9 gene polymorphisms were not significantly associated with the susceptibility to SLE and related phenotypes.
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Affiliation(s)
- J-W Hur
- Department of Internal Medicine, Division of Rheumatology, The Hospital for Rheumatic Diseases, Hanyang University, Seoul, South Korea
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Abstract
BACKGROUND The genetic background of atopic dermatitis (AD) is not clearly understood. Interleukin (IL)-10 is a powerful Th-2 cell cytokine produced by lymphoid cells that exerts its function by inhibiting macrophage/monocyte and T-cell lymphocyte replication and secretion of inflammatory cytokines [IL-1, tumour necrosis factor-alpha (TNFA), IL-6, IL-8 and IL-12]. OBJECTIVE In an effort to discover additional polymorphism(s) in genes whose variant(s) have been implicated in total immunoglobulin E (IgE) level in AD patients, we scrutinized the single nucleotide polymorphisms (SNPs) in the IL10 gene as a potent candidate for contributing to the level of IgE in serum. METHODS We recruited 334 AD patients and assayed their serum total IgE levels using the LIPA-200 system. Four SNPs in the IL10 gene were genotyped using the single-base extension (SBE) method. Logistic regression analyses were performed with single polymorphisms and haplotypes (ht) to determine their association with the level of serum total IgE. RESULTS Genetic association analysis of total serum IgE in AD patients revealed that one of the IL10 ht, IL10-ht2, was associated with decreased serum total IgE in gene dose-dependent manner (P = 0.02-0.001). CONCLUSIONS It was predicted that the inhibition of innate immunity by increased IL-10 production in IL10-ht2-bearing individuals might be associated with decreased total serum IgE levels among AD patients. The greater effects of IL10 ht on decreased total serum IgE levels suggest that the effect of IL-10 polymorphism might be the result of a combined genotype (ht) rather than single polymorphisms.
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Affiliation(s)
- H D Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
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Moon MK, Cho YM, Jung HS, Park YJ, Yoon KH, Sung YA, Park BL, Lee HK, Park KS, Shin HD. Genetic polymorphisms in peroxisome proliferator-activated receptor gamma are associated with Type 2 diabetes mellitus and obesity in the Korean population. Diabet Med 2005; 22:1161-6. [PMID: 16108843 DOI: 10.1111/j.1464-5491.2005.01599.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS We examined whether the common polymorphisms of the peroxisome proliferator-activated receptor-gamma (PPARgamma) gene are associated with Type 2 diabetes or obesity in the Korean population. METHODS We genotyped two common PPARgamma polymorphisms (Pro12Ala and 161C > T) and examined their association with the clinical phenotypes found in 684 patients with Type 2 diabetes mellitus and 291 non-diabetic control subjects. RESULTS The 12Ala allele was less frequent in the Type 2 diabetic patients than in the non-diabetic control subjects (0.036 vs. 0.053, P = 0.024). The allele frequencies of the 161C > T polymorphism did not differ between the control and Type 2 diabetic group (0.158 vs. 0.173). In the non-diabetic controls, those with the T allele had lower BMI and fasting serum triglyceride (TG) concentrations than those with the C/C homozygote (22.7 +/- 2.9 vs. 23.8 +/- 3.2 kg/m2, P = 0.002; 1.45 +/- 0.81 vs. 1.65 +/- 0.83 mmol/l, P = 0.03, respectively). The 12Ala-161T haplotype was associated with a decreased risk for Type 2 diabetes (OR = 0.47, P = 0.009), whereas the 12Pro-161T haplotype was associated with lower BMI and lower fasting serum TG (22.5 +/- 2.8 vs. 23.7 +/- 3.2 kg/m2, P = 0.004; 1.41 +/- 0.87 vs. 1.64 +/- 0.79 mmol/l, P = 0.02, respectively). CONCLUSIONS The PPARgamma 12Ala allele was associated with a reduced risk of Type 2 diabetes, whereas the PPARgamma 161T allele was associated with lower BMI and fasting serum TG concentrations in the Korean subjects. The subjects with 12Ala-161T haplotypes had a reduced risk of Type 2 diabetes.
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Affiliation(s)
- M K Moon
- Department of Internal Medicine, Seoul National University College of Medicine, Chongno-Gu, Seoul, Korea
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Kim JH, Shin HD, Park BL, Cho YM, Kim SY, Lee HK, Park KS. Peroxisome proliferator-activated receptor gamma coactivator 1 alpha promoter polymorphisms are associated with early-onset type 2 diabetes mellitus in the Korean population. Diabetologia 2005; 48:1323-30. [PMID: 15937669 DOI: 10.1007/s00125-005-1793-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2004] [Accepted: 02/28/2005] [Indexed: 11/28/2022]
Abstract
AIMS/HYPOTHESIS Peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1alpha) is a transcriptional coactivator implicated in insulin release by beta cells and in insulin resistance. Therefore, genetic variation of PPARGC1A could be implicated in the onset of type 2 diabetes. In this study, we examined whether the PPARGC1A gene locus is associated with type 2 diabetes mellitus. We also investigated its association with clinical and metabolic parameters in healthy and diabetic subjects. METHODS After sequencing exons and their boundaries of the PPARGC1A gene, including the promoter region ( approximately 1.5 kb), we genotyped eight common single nucleotide polymorphisms (SNPs) in an association study comprising 762 unrelated patients with type 2 diabetes and 303 non-diabetic control patients. We divided the patients with type 2 diabetes into quartiles or three groups according to age at diagnosis of type 2 diabetes (early-onset: <40 years of age, average-onset: 40< or = <60 years, and late-onset: > or =60 years). RESULTS There was no strong association between SNPs or haplotypes of PPARGC1A and type 2 diabetes. However, the SNPs of g.-1789G>A and g.-1437C>T were associated with the age at diagnosis of type 2 diabetes (p=0.042 and p=0.032, respectively). In addition, the promoter SNPs of g.-1789G>A and g.-1437C>T and the haplotypes ht2 (-1789A and -1437T) were significantly associated with early-onset type 2 diabetes (p=0.002, p=0.001 and p=0.001, respectively). CONCLUSIONS/INTERPRETATION Our results suggest that PPARGC1A promoter polymorphisms are associated with age at diagnosis of type 2 diabetes and early-onset type 2 diabetes in the Korean population.
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Affiliation(s)
- J H Kim
- Department of Internal Medicine, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-744, South Korea
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Shin HD, Kim LH, Park BL, Choi YH, Park HS, Hong SJ, Choi BW, Lee JH, Park CS. Association of interleukin 18 (IL18) polymorphisms with specific IgE levels to mite allergens among asthmatic patients. Allergy 2005; 60:900-6. [PMID: 15932380 DOI: 10.1111/j.1398-9995.2005.00619.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Allergy is regarded as a multifactorial condition. Its onset and severity are influenced by both genetic and environmental factors. Identification of genetic factors involved in asthma development and related phenotypes is a major task in understanding the genetic background of asthma. The possible involvement of IL18 polymorphisms in asthma was examined in a Korean asthma cohort. METHODS Direct sequencing was performed to discover single-nucleotide polymorphisms (SNPs) in the IL18 gene. Single-base extension (SBE) method was employed for genotyping. Genotypic influence of IL18 was analysed using logistic and multiple-regression models. RESULTS Although no polymorphisms in the IL18 gene showed significant association with the risk of asthma development, analyses of the association with specific serum IgE levels to Dermatophagoides farinae (D.f.) and D. pteronyssinus (D.p.) among asthmatic patients revealed significant associations with two completely linked SNPs, i.e. -148G>C and +13925A>C(Ser35Ser) (P = 0.01-0.11 for D.f. and P = 0.005-0.11 for D.p.). Both C allele of -148G>C and C allele of +13925A>C showed gene dose-dependent effects on the levels of specific IgE. The lowest IgE levels in homozygotes of minor alleles (1.13 and 1.22 of D.f.; 1.38 and 1.33 of D.p., respectively), intermediate IgE levels in heterozygotes (1.60 and 1.70 of D.f.; 1.84 and 1.92 of D.p., respectively), and the highest levels in homozygotes for major allele (1.93 and 1.93 of D.f.; 2.24 and 2.24 of D.p., respectively), were found. CONCLUSION The genetic relevance of IL18 to specific IgE might offer an important step in understanding the genetic background of allergic diseases.
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Affiliation(s)
- H D Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., MaeHun B/D, Seoul, South Korea
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