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Chung GE, Shin E, Kwak MS, In Yang J, Lee JE, Choe EK, Yim JY. The association of genetic polymorphisms with nonalcoholic fatty liver disease in a longitudinal study. BMC Gastroenterol 2020; 20:344. [PMID: 33059586 PMCID: PMC7565807 DOI: 10.1186/s12876-020-01469-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/24/2020] [Indexed: 12/23/2022] Open
Abstract
Background Several genetic variants are known to be associated with nonalcoholic fatty liver disease (NAFLD). We aimed to evaluate the longitudinal associations between genetic variants and NAFLD. Methods We performed a genome-wide association study (GWAS) in Korean individuals who underwent repeated health check-ups. NAFLD was defined by ultrasonography and exclusion of secondary causes. Results The subjects had a median age of 50.0 years, and 54.8% were male. The median follow-up duration was 39 months. Among the 3905 subjects without NAFLD at baseline, 874 (22.4%) subjects developed NAFLD, and among the 1818 subjects with NAFLD at baseline, NAFLD regressed in 336 (18.5%) subjects during the follow-up period. After adjusting for age, sex and body mass index, no single-nucleotide polymorphism (SNP) passed Bonferroni correction for genome-wide significance in the development or regression of NAFLD. Among the SNPs that passed the genome-wide suggestiveness threshold (p = 1E-04) in the discovery set in the GWAS, only 1 SNP (rs4906353) showed an association with the development of NAFLD, with marginal significance in the validation set (p-value, discovery set = 9.68E-5 and validation set = 0.00531). Conclusions This exploratory study suggests that longitudinal changes in NAFLD are not associated with genetic variants in the Korean population. These findings provide new insight into genetic mechanisms in the pathogenesis of NAFLD.
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Affiliation(s)
- Goh Eun Chung
- Department of Internal Medicine, Gangnam Healthcare Center, Seoul National University Hospital, 39FL., Gangnam Finance center 737, Yeoksam-Dong, Gangnam-Gu, Seoul, 135-984, South Korea.
| | | | - Min-Sun Kwak
- Department of Internal Medicine, Gangnam Healthcare Center, Seoul National University Hospital, 39FL., Gangnam Finance center 737, Yeoksam-Dong, Gangnam-Gu, Seoul, 135-984, South Korea
| | - Jong In Yang
- Department of Internal Medicine, Gangnam Healthcare Center, Seoul National University Hospital, 39FL., Gangnam Finance center 737, Yeoksam-Dong, Gangnam-Gu, Seoul, 135-984, South Korea
| | | | - Eun Kyung Choe
- Healthcare Research Institute, Seoul National University Hospital, Healthcare System Gangnam Center, Seoul, South Korea
| | - Jeong Yoon Yim
- Department of Internal Medicine, Gangnam Healthcare Center, Seoul National University Hospital, 39FL., Gangnam Finance center 737, Yeoksam-Dong, Gangnam-Gu, Seoul, 135-984, South Korea
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A genome-wide association study on liver enzymes in Korean population. PLoS One 2020; 15:e0229374. [PMID: 32084209 PMCID: PMC7034899 DOI: 10.1371/journal.pone.0229374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 02/05/2020] [Indexed: 12/20/2022] Open
Abstract
Background Although genetic features vary across ethnicities, few genome-wide association studies (GWAS) have reported the genetic determinants of liver enzyme expression. This study was aimed to evaluate the associations of genome-wide single nuclear polymorphisms (SNPs) with the liver enzymes in a Korean population. Methods We performed a GWAS to identify genetic loci influencing liver function, as measured by concentrations of alkaline phosphatase (ALP), alanine transaminase (ALT), gamma-glutamyl transferase (GGT) and total bilirubin (BIL) in in Korean study participants. Results A total of 6,488 subjects (4,457 in the discovery and 2,031 in the validation set) were included. The mean subject age was 50.0±10.6 years (male, 53.7%). Among a total of 546,738 SNPs tested, rs651007 and rs579459 located in the ABO gene showed strong associations with ALP (P = 1.63×10−8 and 5.61×10−8, respectively [discovery set]; P = 4.08×10−15 and 9.92×10−16, respectively [validation set]). Additionally, rs5751901 and rs2006092, which are located in the GGT1 gene, showed strong associations with GGT (P = 6.44×10−15 and 1.26×10−15, respectively [discovery set]; P = 4.13×10−10 and 5.15×10−11, respectively [validation set]). Among the 13 SNPs that showed genome-wide significance with total bilirubin levels, rs10929302 and rs6742078 showed the most significant association (P = 3.08×10−64 and 2.05×10−62, respectively [discovery set]; P = 1.33×10−116 and 2.24×10−118, respectively [validation set]). No genome-wide significant associations was found for ALT. Conclusions We demonstrated that ABO, GGT1 and UGT1A family were associated with ALP, GGT and BIL, respectively in Korean population. These findings differ from reported results in GWAS in European populations in terms of associated genes and locations, suggesting different genetic mechanisms of liver enzyme regulation according to ethnicity.
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Chung S, Roh EY, Park B, Lee Y, Shin S, Yoon JH, Song EY. GWAS identifying HLA-DPB1 gene variants associated with responsiveness to hepatitis B virus vaccination in Koreans: Independent association of HLA-DPB1*04:02 possessing rs1042169 G - rs9277355 C - rs9277356 A. J Viral Hepat 2019; 26:1318-1329. [PMID: 31243853 DOI: 10.1111/jvh.13168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Recently, HLA class II loci, including HLA-DPB1, have been reported to be associated with interindividual variance in the hepatitis B (HB) vaccine response. In this study, we investigated significant single nucleotide polymorphisms (SNPs) for anti-HBs antibody levels in 6867 healthy Koreans using a genome-wide association study (GWAS). In GWAS, the top 20 SNPs that showed significant association with anti-HBs levels (P < 1.0 × 10-29 ) all resided in HLA-DPB1. Utilizing PCR sequencing, we verified the relationship of the top 3 most significant SNPs (rs1042169, rs9277355 and rs9277356) from the GWAS and genotypes of HLA-DPB1 with the HB vaccine response in Korean infants who received a scheduled vaccination. The DPB1*04:02 allele has G, C and A nucleotides for the 3SNP sites, and was significantly more frequent in responders than in nonresponders (10.9% vs 1.0%, Pc = 0.018). DPB1*05:01 was significantly more frequent in nonresponders than in responders (49.0% vs 31.1%, Pc = 0.018). In multivariate logistic regression, DPB1*04:02 showed a significant association with both vaccine response (P = 0.037, OR = 8.465) and high-titre response (P = 0.027, OR = 9.860). The haplotypes rs1042169 G - rs9277355 C - rs9277356 A showed a significant association with a high-titre response only (P = 0.002, OR = 2.941). In conclusion, DPB1*04:02 possessing rs1042169 G - rs9277355 C - rs9277356 A is an independent predictor of the HB vaccine response in Koreans.
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Affiliation(s)
- Soie Chung
- Department of Laboratory Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.,Seoul Metropolitan Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea
| | - Boram Park
- Department of Public Health Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yunhwan Lee
- Department of Public Health Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.,Seoul Metropolitan Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.,Seoul Metropolitan Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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Hwangbo Y, Lee EK, Son HY, Im SW, Kwak SJ, Yoon JW, Kim MJ, Kim J, Choi HS, Ryu CH, Lee YJ, Kim JI, Cho NH, Park YJ. Genome-Wide Association Study Reveals Distinct Genetic Susceptibility of Thyroid Nodules From Thyroid Cancer. J Clin Endocrinol Metab 2018; 103:4384-4394. [PMID: 30099483 DOI: 10.1210/jc.2017-02439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/01/2018] [Indexed: 01/02/2023]
Abstract
CONTEXT Thyroid nodules are very common, and 7% to 15% of them are diagnosed as thyroid cancer. However, the inherited genetic risk factors for thyroid nodules and their associations with thyroid cancer remain unknown. OBJECTIVE To identify the genetic variants associated with susceptibility to thyroid nodules in comparison with thyroid cancer. DESIGN AND SETTING We performed a three-stage genome-wide association study for thyroid nodules. The discovery stage involved a genome-wide scan of 811 subjects with thyroid nodules and 691 subjects with a normal thyroid from a population-based cohort. Replication studies were conducted in an additional 1981 cases and 3100 controls from the participants of a health checkup. We also performed expression quantitative trait loci analysis of public data. RESULTS The most robust association was observed in TRPM3 (rs4745021) in the joint analysis (OR, 1.26; P = 6.12 × 10-8) and meta-analysis (OR, 1.28; P = 2.11 × 10-8). Signals at MBIP/NKX2-1 were replicated but did not reach genome-wide significance in the joint analysis (rs2415317, P = 4.62 × 10-5; rs944289, P = 8.68 × 10-5). The expression quantitative trait loci analysis showed that TRPM3 expression was associated with the rs4745021 genotype in thyroid tissues. CONCLUSIONS To the best of our knowledge, we have performed the first genome-wide association study of thyroid nodules and identified a susceptibility locus associated with thyroid nodules, suggesting that thyroid nodules have a genetic predisposition distinct from that of thyroid cancer.
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Affiliation(s)
- Yul Hwangbo
- Center for Thyroid Cancer, National Cancer Center, Korea, Goyang, Republic of Korea
| | - Eun Kyung Lee
- Center for Thyroid Cancer, National Cancer Center, Korea, Goyang, Republic of Korea
| | - Ho-Young Son
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Sun-Wha Im
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Soo-Jung Kwak
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Ji Won Yoon
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Republic of Korea
| | - Min Joo Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Republic of Korea
| | - Jeongseon Kim
- Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Hoon Sung Choi
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, Republic of Korea
| | - Chang Hwan Ryu
- Center for Thyroid Cancer, National Cancer Center, Korea, Goyang, Republic of Korea
| | - You Jin Lee
- Center for Thyroid Cancer, National Cancer Center, Korea, Goyang, Republic of Korea
| | - Jong-Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Nam H Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Young Joo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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Chung GE, Lee Y, Yim JY, Choe EK, Kwak MS, Yang JI, Park B, Lee JE, Kim JA, Kim JS. Genetic Polymorphisms of PNPLA3 and SAMM50 Are Associated with Nonalcoholic Fatty Liver Disease in a Korean Population. Gut Liver 2018; 12:316-323. [PMID: 29271184 PMCID: PMC5945263 DOI: 10.5009/gnl17306] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 12/14/2022] Open
Abstract
Background/Aims The development of nonalcoholic fatty liver disease (NAFLD) is associated with multiple genetic and environmental factors. Methods We performed a genome-wide association study to identify the genetic factors related to NAFLD in a Korean population-based sample of 1,593 subjects with NAFLD and 2,816 controls. We replicated the data in another sample that included 744 NAFLD patients and 1,137 controls. We investigated single-nucleotide polymorphisms (SNPs) that were related to NAFLD. Results After adjusting for age, sex and body mass index, rs738409, rs12483959 and rs2281135, located in the PNPLA3 gene, were validated in our population (p<8.56×10−8) in the same linkage disequilibrium block. Additionally, rs2143571, rs3761472, and rs2073080 in the SAMM50 gene showed significant associations with NAFLD (p<8.56×10−8). Furthermore, these six SNPs showed significant associations with the severity of fatty liver (all p<2.0×10−10 in the discovery set and p<2.0×10−6 in the validation set) and NAFLD, with elevated levels of alanine aminotransferase (all p<2.0×10−10 in the discovery set and p<2.0×10−6 in the validation set). Conclusions We demonstrated that the PNPLA3 and SAMM50 genes are significantly associated with the presence and severity of NAFLD in a Korean population. These findings confirm the important roles of genetic factors in the pathogenesis of NAFLD.
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Affiliation(s)
- Goh Eun Chung
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Young Lee
- Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Jeong Yoon Yim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Eun Kyung Choe
- Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Min-Sun Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jong In Yang
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Boram Park
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | | | | | - Joo Sung Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Genetic Polymorphisms Associated with the Neutrophil⁻Lymphocyte Ratio and Their Clinical Implications for Metabolic Risk Factors. J Clin Med 2018; 7:jcm7080204. [PMID: 30096757 PMCID: PMC6111840 DOI: 10.3390/jcm7080204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Background: The neutrophil–lymphocyte ratio (NLR) is a valuable prognostic or predictive biomarker in various diseases, but the genetic factors that underlie the NLR have not been studied. We attempted to investigate polymorphisms related to NLR phenotype and analyze their ability to predict metabolic risks. Methods: A genome-wide association study was performed with log-transformed NLR using an Affymetrix Axiom™ KORV1.1-96 Array. Regression models for metabolic risk status were designed using the identified significant single-nucleotide polymorphisms (SNPs). Results: We identified four SNPs near the TMEM116, NAA25, and PTPN11 genes that were associated with the NLR. The top SNP associated with the log-transformed NLR was rs76181728 in TMEM116. A case–control study was performed to analyze the metabolic risks associated with each SNP after adjusting for age, sex, and body mass index (BMI). Three SNPs displayed significant odds ratios (ORs) for increased blood pressure and increased waist circumference. In the regression model for metabolic syndrome, rs76181728 showed a significant association (OR = 1.465, 95% confidence interval (CI) = 1.091–1.969, P = 0.011) after adjustment for the NLR phenotype. Conclusions: We identified four novel SNPs that are associated with the NLR in healthy Koreans. SNPs in relevant genes might therefore serve as biomarkers for metabolic risks.
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Genome-wide assessment of gene-by-smoking interactions in COPD. Sci Rep 2018; 8:9319. [PMID: 29915320 PMCID: PMC6006158 DOI: 10.1038/s41598-018-27463-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/30/2018] [Indexed: 12/14/2022] Open
Abstract
Cigarette smoke exposure is a major risk factor in chronic obstructive pulmonary disease (COPD) and its interactions with genetic variants could affect lung function. However, few gene-smoking interactions have been reported. In this report, we evaluated the effects of gene-smoking interactions on lung function using Korea Associated Resource (KARE) data with the spirometric variables—forced expiratory volume in 1 s (FEV1). We found that variations in FEV1 were different among smoking status. Thus, we considered a linear mixed model for association analysis under heteroscedasticity according to smoking status. We found a previously identified locus near SOX9 on chromosome 17 to be the most significant based on a joint test of the main and interaction effects of smoking. Smoking interactions were replicated with Gene-Environment of Interaction and phenotype (GENIE), Multi-Ethnic Study of Atherosclerosis-Lung (MESA-Lung), and COPDGene studies. We found that individuals with minor alleles, rs17765644, rs17178251, rs11870732, and rs4793541, tended to have lower FEV1 values, and lung function decreased much faster with age for smokers. There have been very few reports to replicate a common variant gene-smoking interaction, and our results revealed that statistical models for gene-smoking interaction analyses should be carefully selected.
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