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Pasaje CFA, Kim JH, Park BL, Cheong HS, Bae JS, Park TJ, Lee JS, Kim Y, Lee HS, Koh I, Kim YJ, Shin HD. Lack of association of RAD51 genetic variations with hepatitis B virus clearance and occurrence of hepatocellular carcinoma in a Korean population. J Med Virol 2012; 83:1892-9. [PMID: 21915862 DOI: 10.1002/jmv.22122] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The RecA homolog, E. coli (S. cerevisiae) (RAD51) may modulate hepatitis B virus (HBV) infection by maintaining genome integrity and mediating homologous DNA repairs. In this study, 16 sequence variations were detected by resequencing all exons, the exon-intron boundary, and promoter regions of the human RAD51 gene in DNA samples of 24 unrelated individuals. To investigate the association of common variations in the RAD51 locus with HBV infection and hepatocellular carcinoma (HCC) occurrence, six common polymorphisms were genotyped in a total of 1,103 Korean HBV cohort, composed of 433 spontaneously recovered patients as controls and 670 chronic carriers of HBV, who were stratified further into 327 cirrhosis/chronic hepatitis patients and 343 patients with HCC infected with HBV. Logistic analyses revealed no significant association of RAD51 polymorphisms and haplotypes with HBV clearance and HCC occurrence (P > 0.05). Furthermore, with age of infection as an important factor in disease progression to HCC, results from the Cox proportional hazards analysis showed no significant associations between any of the tested RAD51 variants and the age of onset of HCC (P > 0.05), suggesting that genetic polymorphisms of RAD51 may not play an important role in clearance of HBV and disease progression to HCC. Although studies in other populations are needed to confirm these findings, this preliminary data may contribute to the current knowledge on the pathogenesis of hepatitis.
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Pasaje CFA, Bae JS, Park BL, Cheong HS, Kim JH, Jang AS, Uh ST, Park CS, Shin HD. Possible role of EMID2 on nasal polyps pathogenesis in Korean asthma patients. BMC MEDICAL GENETICS 2012; 13:2. [PMID: 22217332 PMCID: PMC3398310 DOI: 10.1186/1471-2350-13-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 01/04/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Since subepithelial fibrosis and protruded extracellular matrix are among the histological characteristics of polyps, the emilin/multimerin domain-containing protein 2 (EMID2) gene is speculated to be involved in the presence of nasal polyps in asthma and aspirin-hypersensitive patients. METHODS To investigate the association between EMID2 and nasal polyposis, 49 single-nucleotide polymorphisms (SNPs) were genotyped in 467 asthmatics of Korean ancestry who were stratified further into 114 aspirin exacerbated respiratory disease (AERD) and 353 aspirin-tolerant asthma (ATA) subgroups. From pairwise comparison of the genotyped polymorphisms, 14 major haplotypes (frequency > 0.05) were inferred and selected for association analysis. Differences in the frequency distribution of EMID2 variations between polyp-positive cases and polyp-negative controls were determined using logistic analyses. RESULTS Initially, 13 EMID2 variants were significantly associated with the presence of nasal polyps in the overall asthma group (P = 0.0008-0.05, OR = 0.54-1.32 using various modes of genetic inheritance). Although association signals from 12 variants disappeared after multiple testing corrections, the relationship between EMID2_BL1_ht2 and nasal polyposis remained significant via a codominant mechanism (P corr = 0.03). On the other hand, the nominal associations observed between the genetic variants tested for the presence of nasal polyps in AERD (P = 0.003-0.05, OR = 0.25-1.82) and ATA (P = 0.01-0.04, OR = 0.46-10.96) subgroups disappeared after multiple comparisons, suggesting lack of associations. CONCLUSIONS These preliminary findings suggest that EMID2_BL1_ht2 may be a susceptibility marker of inflammation of the nasal passages among Korean asthma patients.
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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] [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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Pasaje CFA, Bae JS, Park BL, Kim JH, Cheong HS, Uh ST, Park CS, Shin HD. Genetic variations in KIFC1 and the risk of aspirin exacerbated respiratory disease in a Korean population: an association analysis. Mol Biol Rep 2011; 39:5913-9. [PMID: 22201025 DOI: 10.1007/s11033-011-1403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 12/17/2011] [Indexed: 11/29/2022]
Abstract
Modest effects of genes in various pathways are significant in the etiology of complex human diseases, including aspirin exacerbated respiratory disease (AERD). By functioning as a relevant component of respiratory processes, the human kinesin family member C1 (KIFC1) is hypothesized to play a role in AERD pathogenesis. A case-control analysis was carried out by comparing the genotype distribution of six KIFC1 single-nucleotide polymorphisms between 93 AERD cases and 96 aspirin-tolerant asthma controls in a Korean population. After controlling for confounds, logistic and regression models via various modes of genetic inheritance facilitated the association analysis. Initial results revealed significant association at 0.05 level of significance between several KIFC1 variations and AERD (P = 0.01-0.05, OR = 1.81-1.90) as well as fall rate of forced expiratory volume in the 1st second, an important diagnostic marker of airways constriction (P = 0.04-0.05). However, the signals were not deemed significant after multiple testing corrections (P (corr) > 0.05). Although the results do not support a major role of KIFC1 in AERD pathogenesis in a Korean asthma cohort, further replication and validation studies are required to clarify the current findings.
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Lee JS, Bae JS, Kim JH, Kim JY, Park TJ, Pasaje CFA, Park BL, Cheong HS, Uh ST, Park JS, Park CS, Shin HD. Effect of diffuse panbronchiolitis critical region 1 polymorphisms on the risk of aspirin-exacerbated respiratory disease in Korean asthmatics. Respir Care 2011; 57:758-63. [PMID: 22152429 DOI: 10.4187/respcare.01480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The functional role of the human diffuse panbronchiolitis critical region 1 (DPCR1) gene, located in the major histocompatibility complex class I, has not been widely investigated. However, this gene is a well known genetic marker for diffuse panbronchiolitis, a disease affecting human respiratory bronchioles. In this study we explored the association between polymorphisms in DPCR1 and aspirin-exacerbated respiratory disease (AERD), an asthma phenotype. METHODS Genotyping of 6 polymorphisms was carried out in a total of 189 Korean asthmatic patients stratified into 93 AERD cases and 96 aspirin tolerant asthma controls. Subjects who exhibited significant decrease of FEV(1) by aspirin provocation were identified as AERD subjects. Logistic and regression analyses were performed to investigate the association between DPCR1 polymorphisms and the risk of AERD as well as FEV(1) decline. RESULTS Initial analysis revealed significant association of rs2517449 with AERD, with a P value of .03 via a recessive model; however, the association signal disappeared after multiple testing corrections. In addition, rs2517449 and rs2240804 also showed association signals with decline of FEV(1) after aspirin provocation (P = .007 and .03, respectively, in a recessive model). After testing for multiple comparisons, only the association signal from rs2517449 was retained (P(corr) = .04), while other polymorphisms showed no associations with the risk of AERD and FEV(1) decline. CONCLUSIONS Our results show that polymorphisms in DPCR1 are not associated with the risk of AERD.
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Lee JS, Bae JS, Park BL, Cheong HS, Kim JH, Pasaje CFA, Kim JY, Park TJ, Uh ST, Park CS, Shin HD. Lack of association of HLA-DRA polymorphisms with aspirin exacerbated respiratory disease in a Korean population. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jin XR, Park J, Zheng H, Lee S, Lee Y, Rhee JY, Kim KW, Cheong HS, Jang WH. Highly-dispersive transparency at optical frequencies in planar metamaterials based on two-bright-mode coupling. OPTICS EXPRESS 2011; 19:21652-21657. [PMID: 22109014 DOI: 10.1364/oe.19.021652] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Using a planar metamaterial, which consists of two silver strips, we theoretically demonstrate the plasmonic electromagnetically-induced transparency (EIT)-like spectral response at optical frequencies. The two silver strips serve as the bright modes, and are excited strongly by the incident wave. Based on the weak hybridization between the two bright modes, a highly-dispersive plasmonic EIT-like spectral response appears in our scheme. Moreover, the group index is higher than that of another scheme which utilizes the strong coupling between the bright and dark modes.
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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. Genetic analysis between FGD6 and aspirin exacerbated respiratory disease in a Korean population. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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 AND BEHAVIOR 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] [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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Kim JH, Yu SJ, Park BL, Cheong HS, Pasaje CFA, Bae JS, Lee HS, Shin HD, Kim YJ. TGFBR3 polymorphisms and its haplotypes associated with chronic hepatitis B virus infection and age of hepatocellular carcinoma occurrence. Dig Dis 2011; 29:278-83. [PMID: 21829018 DOI: 10.1159/000327559] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC) is one of the most common cancers and is mainly caused by viral infections including hepatitis B virus (HBV). Recently, the decreased expression level of the transforming growth factor, beta receptor III (TGFBR3) gene, has been implicated in HCC and other human cancers. This study investigated whether TGFBR3 polymorphisms might be associated with HBV clearance and HCC occurrence. METHODS This study identified 27 single nucleotide polymorphisms (SNPs) in the exon, promoter, and exon-intron boundary regions of TGFBR3 by resequencing in 24 individuals. Then, 9 SNPs in the promoter and exons of the gene were genotyped from 1,065 Koreans composed of 637 chronic carriers (CC) and 428 spontaneously recovered (SR) subjects. RESULTS Two SNPs, rs1805113 (Phe676Phe) in exon 13 and rs1805117 in 3'-UTR (p = 0.009 and p = 0.008, respectively) were significantly associated with HBV clearance. In addition, Cox relative hazards analyses revealed that haplotype BL2_ht2 showed a significant association with the age of HCC occurrence among chronic HBV patients (relative hazard = 1.38; p = 0.007). CONCLUSION Our findings suggest that TGFBR3 polymorphisms and its haplotypes might be associated with HBV clearance and age of HCC occurrence.
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Cheong HS, Kim HD, Na HS, Kim JO, Kim LH, Kim SH, Bae JS, Chung MW, Shin HD. Screening of genetic variations of SLC15A2, SLC22A1, SLC22A2 and SLC22A6 genes. J Hum Genet 2011; 56:666-70. [DOI: 10.1038/jhg.2011.77] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bae JS, Jung MH, Lee BC, Cheong HS, Park BL, Kim LH, Kim JH, Pasaje CFA, Lee JS, Jung KH, Chai YG, Shin HD, Choi IG. The Genetic Effect of Copy Number Variations on the Risk of Alcoholism in a Korean Population. Alcohol Clin Exp Res 2011; 36:35-42. [DOI: 10.1111/j.1530-0277.2011.01578.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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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. Lack of association between CD58 genetic variations and aspirin-exacerbated respiratory disease in a Korean population. J Asthma 2011; 48:539-45. [PMID: 21726122 DOI: 10.3109/02770903.2011.589557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Exacerbation of asthma symptoms due to aspirin ingestion may lead to life-threatening lung failure. The adhesion molecule CD58 gene may play a crucial role in aspirin-exacerbated respiratory disease (AERD) pathogenesis by mediating the biological functions of asthma-inducing mechanisms including T helper cells, proinflammatory cytokines, and natural killer T cells. OBJECTIVE This study aimed to investigate the association of CD58 variations with aspirin-induced bronchospasm in Korean asthma patients. METHODS Seven single-nucleotide polymorphisms were selected for genotyping based on previously reported polymorphisms in the International HapMap database. Genotyping was carried out using TaqMan assay and 2 major haplotypes were obtained in 163 AERD cases and 429 aspirin-tolerant asthma controls. Frequency distributions of CD58 variations were analyzed using logistic and regression models. RESULTS Results showed that none of the analyzed CD58 single-nucleotide polymorphisms and haplotypes was significantly associated with AERD development and fall rate of FEV(1) by aspirin provocation, an important diagnostic marker of aspirin hypersensitivity. CONCLUSIONS This preliminary study suggests that CD58 does not affect AERD susceptibility in a Korean population, and may provide a new direction for future disease etiology.
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Kim JY, Cheong HS, Park BL, Baik SH, Park S, Lee SW, Kim MH, Chung JH, Choi JS, Kim MY, Yang JH, Cho DH, Shin HD, Kim SH. Melatonin receptor 1 B polymorphisms associated with the risk of gestational diabetes mellitus. BMC MEDICAL GENETICS 2011; 12:82. [PMID: 21658282 PMCID: PMC3129295 DOI: 10.1186/1471-2350-12-82] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 06/10/2011] [Indexed: 12/29/2022]
Abstract
Backgrounds Two SNPs in melatonin receptor 1B gene, rs10830963 and rs1387153 showed significant associations with fasting plasma glucose levels and the risk of Type 2 Diabetes Mellitus (T2DM) in previous studies. Since T2DM and gestational diabetes mellitus (GDM) share similar characteristics, we suspected that the two genetic polymorphisms in MTNR1B may be associated with GDM, and conducted association studies between the polymorphisms and the disease. Furthermore, we also examined genetic effects of the two polymorphisms with various diabetes-related phenotypes. Methods A total of 1,918 subjects (928 GDM patients and 990 controls) were used for the study. Two MTNR1B polymorphisms were genotyped using TaqMan assay. The allele distributions of SNPs were evaluated by x2 models calculating odds ratios (ORs), 95% confidence intervals (CIs), and corresponding P values. Multiple regressions were used for association analyses of GDM-related traits. Finally, conditional analyses were also performed. Results We found significant associations between the two genetic variants and GDM, rs10830963, with a corrected P value of 0.0001, and rs1387153, with the corrected P value of 0.0008. In addition, we also found that the two SNPs were associated with various phenotypes such as homeostasis model assessment of beta-cell function and fasting glucose levels. Further conditional analyses results suggested that rs10830963 might be more likely functional in case/control analysis, although not clear in GDM-related phenotype analyses. Conclusion There have been studies that found associations between genetic variants of other genes and GDM, this is the first study that found significant associations between SNPs of MTNR1B and GDM. The genetic effects of two SNPs identified in this study would be helpful in understanding the insight of GDM and other diabetes-related disorders.
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Pasaje CFA, Bae JS, Park BL, Cheong HS, Jang AS, Uh ST, Kim MK, Koh IS, Kim JH, Park TJ, Lee JS, Kim Y, Park CS, Shin HD. Association analysis of C6 genetic variations and aspirin hypersensitivity in Korean asthmatic patients. Hum Immunol 2011; 72:973-8. [PMID: 21704099 DOI: 10.1016/j.humimm.2011.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 05/09/2011] [Accepted: 05/20/2011] [Indexed: 02/05/2023]
Abstract
There has been increasing evidence that genetic mechanisms contribute to the development of aspirin-intolerant asthma (AIA), a life-threatening disease. The complement component (C6) is a constituent of a biochemical cascade that has been implicated in airway epithelial damage and nasal polyposis, and therefore, may be a risk factor for AIA. To investigate the association between C6 variations and AIA in a Korean asthma cohort, 27 SNPs were selected for genotyping based on previously reported polymorphisms in the HapMap database. Genotyping was carried out using TaqMan assay, and five major haplotypes were obtained in 163 AIA cases and 429 aspirin-tolerant asthma (ATA) controls subjects. Genotype frequency distributions of C6 polymorphisms and haplotypes were analyzed using logistic and regression models. Subsequent analyses revealed a lack of association between C6 genetic variations and AIA. From the initial analyses, marginal associations of rs10512766 (p = 0.04 in co-dominant model) and rs4957374 (p = 0.05 in dominant model) with AIA did not reach the threshold of significance after multiple testing corrections; thus this study failed to find convincing evidence that variations in C6 gene influence the risk of AIA in a Korean population. However, these preliminary results may contribute to the etiology of aspirin hypersensitivity in Korean asthmatic patients.
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Kim JY, Kim JH, Park TJ, Lee JS, Pasaje CF, Bae JS, Park BL, Cheong HS, Lee HS, Kim YJ, Shin HD. No association of TF gene polymorphisms with hepatitis B virus Clearance and hepatocellular carcinoma occurrence in a Korean population. Genes Genomics 2011. [DOI: 10.1007/s13258-010-0164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pasaje CFA, Kim JH, Park BL, Cheong HS, Park TJ, Lee JS, Kim Y, Bae JS, Kim JM, Park JS, Park CS, Shin HD. Association of the variants in AGT gene with modified drug response in Korean aspirin-intolerant asthma patients. Pulm Pharmacol Ther 2011; 24:595-601. [PMID: 21624492 DOI: 10.1016/j.pupt.2011.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 12/17/2010] [Accepted: 05/14/2011] [Indexed: 11/30/2022]
Abstract
The angiotensinogen (AGT) gene enhances the effect of several bronchoconstrictors and produces a peptide that is accumulated in the airways of asthma patients; events that may underpin the pathogenesis of aspirin-intolerant asthma (AIA). To carry out a case-control analysis between AGT and aspirin-induced bronchospasm following treatment with an anti-asthma drug, montelukast (MLK), 38 single nucleotide polymorphisms (SNPs) in AGT were genotyped in 56 AIA cohort. Genotyping was performed with TaqMan assay and haplotypes were inferred using PHASE algorithm ver. 2.0. Statistical analyses of each SNPs and haplotypes were performed using SAS version 9.1. Among 13 variants displaying significant signals, two SNPs (+2401C>G and +2476C>T) in the intronic region of AGT were significantly associated with modification of drug response even after correction for multiple testing (P=0.0009-0.002; P(corr)=0.02-0.03). Furthermore, the two variants also exhibited associations with MLK response rate (P=0.0003-0.0006; P(corr)=0.006-0.01). Although our results are preliminary and further replication in a larger-scale group of subjects should be warranted, these observations provide evidence that AGT variants might be one of genetic factors involved in the response of anti-asthma drugs in AIA patients.
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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] [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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Bae JS, Cheong HS, Kim JH, Park BL, Kim JH, Park TJ, Kim JY, Pasaje CFA, Lee JS, Park YJ, Park M, Park C, Koh I, Chung YJ, Lee JY, Shin HD. The genetic effect of copy number variations on the risk of type 2 diabetes in a Korean population. PLoS One 2011; 6:e19091. [PMID: 21526130 PMCID: PMC3081314 DOI: 10.1371/journal.pone.0019091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 03/28/2011] [Indexed: 11/19/2022] Open
Abstract
Background Unlike Caucasian populations, genetic factors contributing to the risk of type 2 diabetes mellitus (T2DM) are not well studied in Asian populations. In light of this, and the fact that copy number variation (CNV) is emerging as a new way to understand human genomic variation, the objective of this study was to identify type 2 diabetes–associated CNV in a Korean cohort. Methodology/Principal Findings Using the Illumina HumanHap300 BeadChip (317,503 markers), genome-wide genotyping was performed to obtain signal and allelic intensities from 275 patients with type 2 diabetes mellitus (T2DM) and 496 nondiabetic subjects (Total n = 771). To increase the sensitivity of CNV identification, we incorporated multiple factors using PennCNV, a program that is based on the hidden Markov model (HMM). To assess the genetic effect of CNV on T2DM, a multivariate logistic regression model controlling for age and gender was used. We identified a total of 7,478 CNVs (average of 9.7 CNVs per individual) and 2,554 CNV regions (CNVRs; 164 common CNVRs for frequency>1%) in this study. Although we failed to demonstrate robust associations between CNVs and the risk of T2DM, our results revealed a putative association between several CNVRs including chr15:45994758–45999227 (P = 8.6E-04, Pcorr = 0.01) and the risk of T2DM. The identified CNVs in this study were validated using overlapping analysis with the Database of Genomic Variants (DGV; 71.7% overlap), and quantitative PCR (qPCR). The identified variations, which encompassed functional genes, were significantly enriched in the cellular part, in the membrane-bound organelle, in the development process, in cell communication, in signal transduction, and in biological regulation. Conclusion/Significance We expect that the methods and findings in this study will contribute in particular to genome studies of Asian populations.
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Kim M, Kang TW, Lee HC, Han YM, Kim H, Shin HD, Cheong HS, Lee D, Kim SY, Kim YS. Identification of DNA methylation markers for lineage commitment of in vitro hepatogenesis. Hum Mol Genet 2011; 20:2722-33. [DOI: 10.1093/hmg/ddr171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lee JS, Kim JH, Park BL, Cheong HS, Koh I, Kim JYH, Park TJ, Pasaje CF, Bae JS, Lee HS, Kim YJ, Shin HD. No associations of polymorphisms in ADPRT with hepatitis B virus clearance and hepatocellular carcinoma occurrence in a Korean population. Hepatol Res 2011; 41:250-7. [PMID: 21276153 DOI: 10.1111/j.1872-034x.2010.00772.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
AIM The human adenosine diphosphate ribosyl transferase (ADPRT) gene might significantly affect cancer by encoding poly(ADP-ribose) polymerase 1 enzyme (PARP-1) and promoting an important role in cellular responses to DNA damage, genomic stabilization and regulation of tumor suppressor genes. We explored whether polymorphisms of ADPRT affect clearance of hepatitis B virus (HBV) infection or risk of hepatocellular carcinoma (HCC) occurrence in a Korean HBV cohort. METHODS Genotyping was performed in a total of 1066 subjects composed of 434 spontaneously recovered (SR) subjects as normal controls and 632 chronic carriers (CC) of HBV who were further classified into 325 patients with liver cirrhosis (LC)/chronic hepatitis (CH) and 307 patients with HCC. RESULTS Logistic analyses of six common single nucleotide polymorphisms (SNP) and their haplotypes revealed that none of the polymorphisms were significantly associated with clearance of HBV infection and HCC occurrence, except for nominal evidence of association between haplotype 2 (ht2) with HBV clearance (P = 0.05). In the analysis of age of HCC occurrence which is an important factor in disease progression to HCC, results from Cox proportional hazards showed that none of the variants were significantly associated with onset age of HCC occurrence, although a nominal signal in ht4 (P = 0.03, but P(corr) > 0.05) was initially detected. CONCLUSION Although ADPRT is an important gene for cellular responses and tumor regulations, our study provides evidence that ADPRT variations do not affect HBV clearance and HCC occurrence.
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Park TJ, Kim JH, Bae JS, Park BL, Cheong HS, Chun JY, Lee JS, Kim JY, Pasaje CF, Cho SH, Uh ST, Kim MK, Choi IS, Koh IS, Park CS, Shin HD. Possible association of SLC22A2 polymorphisms with aspirin-intolerant asthma. Int Arch Allergy Immunol 2011; 155:395-402. [PMID: 21346370 DOI: 10.1159/000321267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Aspirin-intolerant asthma (AIA) is a clinical syndrome characterized by acute bronchoconstriction following the ingestion of aspirin. Solute carrier family 22, member 2 (SLC22A2), also known as organic cation transporter 2 (OCT2), is predominantly expressed in the luminal membrane of airway epithelial cells and has been shown to mediate the transport of prostaglandins on the cyclooxygenase pathway which is regulated by aspirin blockage. Recently, SLC22A2-mediated uptake inhibition by several nonsteroidal anti-inflammatory drugs and decreased SLC22A2 transport activity by its genetic variants have been elucidated in asthma. METHODS To investigate the associations between AIA and genetic polymorphisms of the SLC22A2 gene, 18 variants were genotyped in 163 AIA subjects and 429 aspirin-tolerant asthma (ATA) controls. Logistic analyses were used to evaluate p values for the associations of SLC22A2 polymorphisms with AIA. RESULTS One common polymorphism in intron 5, i.e. rs316021, was significantly associated with susceptibility to AIA (p = 0.004, P(corr) = 0.05, OR = 0.60, 95% CI = 0.43-0.85 in a codominant model). The minor allele frequency of rs316021 in the AIA group was significantly lower than that in the ATA controls. In addition, a polymorphism in intron 4 (rs3912161) and a haplotype (SLC22A2-ht3) showed significantly stronger association signals with the FEV(1) fall rate induced by aspirin provocation in AIA subjects compared with ATA controls (p = 0.004, P(corr) = 0.05). CONCLUSION Our findings suggest that SLC22A2 could be a susceptibility gene for aspirin intolerance in asthmatics.
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Lee JS, Kim JH, Bae JS, Kim JY, Park TJ, Pasaje CF, Park BL, Cheong HS, Park JS, Uh ST, Kim MK, Choi IS, Cho SH, Choi BW, Park CS, Shin HD. Association analysis of UBE3C polymorphisms in Korean aspirin-intolerant asthmatic patients. Ann Allergy Asthma Immunol 2011; 105:307-312. [PMID: 20934631 DOI: 10.1016/j.anai.2010.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/06/2010] [Accepted: 07/19/2010] [Indexed: 10/19/2022]
Abstract
BACKGROUND Aspirin-intolerant asthma (AIA), as an asthma phenotype that involves the upper or lower airways, occurs from excessive leukotriene production on administration of nonsteroidal anti-inflammatory drugs. The UBE3C gene on chromosome 7 is a member of the E3 ligase enzymes and is implicated in the ubiquitin-proteasome pathway. This pathway is involved in immune responses to inflammation, including asthma. OBJECTIVE To investigate whether the UBE3C polymorphisms are associated with the risk of AIA. METHODS Twenty-four nonmonomorphic genetic variants of UBE3C were genotyped in 163 patients with AIA and 429 controls with aspirin-tolerant asthma. After genotyping, logistic analyses were performed and haplotypes of each individual were inferred using the PHASE algorithm. RESULTS Logistic analyses revealed that 2 polymorphisms (rs3802122 and rs6979947) in the intron showed significant associations with risk of AIA (P < .001 and P(corr) = .002 in both single nucleotide polymorphisms; odds ratios, 0.61 and 0.60, respectively). In associations with haplotypes, haplotype 2, which contains all the significantly associated single nucleotide polymorphisms and was infrequent in AIA compared with aspirin-tolerant asthma, was associated with aspirin hypersensitivity in asthmatic patients (P = .003 and P(corr) = .03; odds ratio, 0.64; 95% confidence interval, 0.47-0.86). CONCLUSIONS The rs3802122 and rs6979947 polymorphisms were significantly associated with the risk of AIA. However, further studies are required to establish the underlying mechanism by which UBE3C and its polymorphisms affect the risk of AIA.
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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] [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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Cheong HS, Park BL, Kim EM, Park CS, Sohn JW, Kim BJ, Kim JW, Kim KH, Shin TM, Choi IG, Han SW, Hwang J, Koh I, Shin HD, Woo SI. Association of RANBP1 haplotype with smooth pursuit eye movement abnormality. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:67-71. [PMID: 21184585 DOI: 10.1002/ajmg.b.31139] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/30/2010] [Indexed: 11/09/2022]
Abstract
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 RANBP1 polymorphisms with the risk of schizophrenia and with the risk of SPEM abnormality in schizophrenia patients in a Korean population. Two SNPs of RANBP1 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 χ² and multiple regression analyses. Although no RANBP1 polymorphisms were associated with the risk of schizophrenia, a common haplotype, RANBP1-ht2 (rs2238798G-rs175162T), showed significant association with the risk of SPEM abnormality among schizophrenia patients after multiple correction (P(corr) = 0.002-0.0003). The results of present study provide the evidence that RANBP1 on 22q11.21 locus might be causally related to the SPEM abnormality rather than the development of schizophrenia.
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