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Lin WY. Searching for gene-gene interactions through variance quantitative trait loci of 29 continuous Taiwan Biobank phenotypes. Front Genet 2024; 15:1357238. [PMID: 38516378 PMCID: PMC10956579 DOI: 10.3389/fgene.2024.1357238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction: After the era of genome-wide association studies (GWAS), thousands of genetic variants have been identified to exhibit main effects on human phenotypes. The next critical issue would be to explore the interplay between genes, the so-called "gene-gene interactions" (GxG) or epistasis. An exhaustive search for all single-nucleotide polymorphism (SNP) pairs is not recommended because this will induce a harsh penalty of multiple testing. Limiting the search of epistasis on SNPs reported by previous GWAS may miss essential interactions between SNPs without significant marginal effects. Moreover, most methods are computationally intensive and can be challenging to implement genome-wide. Methods: I here searched for GxG through variance quantitative trait loci (vQTLs) of 29 continuous Taiwan Biobank (TWB) phenotypes. A discovery cohort of 86,536 and a replication cohort of 25,460 TWB individuals were analyzed, respectively. Results: A total of 18 nearly independent vQTLs with linkage disequilibrium measure r 2 < 0.01 were identified and replicated from nine phenotypes. 15 significant GxG were found with p-values <1.1E-5 (in the discovery cohort) and false discovery rates <2% (in the replication cohort). Among these 15 GxG, 11 were detected for blood traits including red blood cells, hemoglobin, and hematocrit; 2 for total bilirubin; 1 for fasting glucose; and 1 for total cholesterol (TCHO). All GxG were observed for gene pairs on the same chromosome, except for the APOA5 (chromosome 11)-TOMM40 (chromosome 19) interaction for TCHO. Discussion: This study provided a computationally feasible way to search for GxG genome-wide and applied this approach to 29 phenotypes.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei, Taiwan
- Master of Public Health Degree Program, College of Public Health, National Taiwan University, Taipei, Taiwan
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Shamsudin AF, Bakar NS. Gender Differences in the Association between Cholesteryl Esters Transfer Protein Polymorphism (rs708272) and Plasma Lipid Levels in Hyperlipidaemic Participants at Hospital Universiti Sains Malaysia. Malays J Med Sci 2023; 30:96-110. [PMID: 37102051 PMCID: PMC10125239 DOI: 10.21315/mjms2023.30.2.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 04/09/2022] [Indexed: 04/28/2023] Open
Abstract
Background Single nucleotide polymorphism (SNP) in the cholesteryl esters transfer protein (CETP) gene (rs708272) was reported to affect statin efficacy. This study investigated the association between CETP rs708272 and statin's lipid-lowering effects in hyperlipidaemic participants at Hospital Universiti Sains Malaysia, Kelantan. Methods A total of 229 hyperlipidaemic statin users (96.1% Malays) were recruited, and a single blood sample (3 mL) was obtained for DNA extraction. The genotypes were determined using PCR-RFLP method and validated by sequencing analysis. Results The minor allele frequency for rs708272 in all participants was 0.391, with no difference between females and males. At the baseline, the SNP was associated with different low-density lipoprotein (LDL-c) and triglyceride (TG) levels in females, but not males, when the GG and GA+AA genotypes were compared using a dominant genetic model. Regardless of the genotype, the total cholesterol and LDL-c levels decreased significantly (P < 0.001) in both genders after statin treatment, but the TG levels decreased exclusively in females with the GG genotypes. In both genders, high density lipoprotein levels were unaffected before and after the statin treatment. Conclusion To improve the management of hyperlipidaemia, future research should consider patient gender when assessing the CETP rs708272 impact on LDL-c and TG.
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Affiliation(s)
| | - Nur Salwani Bakar
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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Pan X. The Roles of Fatty Acids and Apolipoproteins in the Kidneys. Metabolites 2022; 12:metabo12050462. [PMID: 35629966 PMCID: PMC9145954 DOI: 10.3390/metabo12050462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
The kidneys are organs that require energy from the metabolism of fatty acids and glucose; several studies have shown that the kidneys are metabolically active tissues with an estimated energy requirement similar to that of the heart. The kidneys may regulate the normal and pathological function of circulating lipids in the body, and their glomerular filtration barrier prevents large molecules or large lipoprotein particles from being filtered into pre-urine. Given the permeable nature of the kidneys, renal lipid metabolism plays an important role in affecting the rest of the body and the kidneys. Lipid metabolism in the kidneys is important because of the exchange of free fatty acids and apolipoproteins from the peripheral circulation. Apolipoproteins have important roles in the transport and metabolism of lipids within the glomeruli and renal tubules. Indeed, evidence indicates that apolipoproteins have multiple functions in regulating lipid import, transport, synthesis, storage, oxidation and export, and they are important for normal physiological function. Apolipoproteins are also risk factors for several renal diseases; for example, apolipoprotein L polymorphisms induce kidney diseases. Furthermore, renal apolipoprotein gene expression is substantially regulated under various physiological and disease conditions. This review is aimed at describing recent clinical and basic studies on the major roles and functions of apolipoproteins in the kidneys.
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Affiliation(s)
- Xiaoyue Pan
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, New York, NY 11501, USA;
- Diabetes and Obesity Research Center, NYU Langone Hospital—Long Island, Mineola, New York, NY 11501, USA
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Takeuchi K, Naito M, Kawai S, Tsukamoto M, Kadomatsu Y, Kubo Y, Okada R, Nagayoshi M, Tamura T, Hishida A, Nakatochi M, Sasakabe T, Hashimoto S, Eguchi H, Momozawa Y, Ikezaki H, Murata M, Furusyo N, Tanaka K, Hara M, Nishida Y, Matsuo K, Ito H, Oze I, Mikami H, Nakamura Y, Kusakabe M, Takezaki T, Ibusuki R, Shimoshikiryo I, Suzuki S, Nishiyama T, Watanabe M, Koyama T, Ozaki E, Watanabe I, Kuriki K, Kita Y, Ueshima H, Matsui K, Arisawa K, Uemura H, Katsuura-Kamano S, Nakamura S, Narimatsu H, Hamajima N, Tanaka H, Wakai K. Study profile of the Japan Multi-institutional Collaborative Cohort (J-MICC) Study. J Epidemiol 2020; 31:660-668. [PMID: 32963210 PMCID: PMC8593573 DOI: 10.2188/jea.je20200147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Japan Multi-institutional Collaborative Cohort (J-MICC) study was launched in 2005 to examine gene-environment interactions in lifestyle-related diseases, including cancers, among the Japanese. This report describes the study design and baseline profile of the study participants. METHODS The participants of the J-MICC Study were individuals aged 35 to 69 years enrolled from respondents to study announcements in specified regions, inhabitants attending health checkup examinations provided by local governments, visitors at health checkup centers, and first-visit patients at a cancer hospital in Japan. At the time of the baseline survey, from 2005 to 2014, we obtained comprehensive information regarding demographics, education, alcohol consumption, smoking, sleeping, exercise, food intake frequency, medication and supplement use, personal and family disease history, psychological stress, and female reproductive history, and collected peripheral blood samples. RESULTS The baseline survey included 92,610 adults (mean age: 55.2 [9.4] years, 44.1% men) from 14 study regions in 12 prefectures. The participation rate was 33.5%, with participation ranging from 19.7% to 69.8% in different study regions. The largest number of participants was in the age groups of 65-69 years for men and 60-64 years for women. There were differences in body mass index, educational attainment, alcohol consumption, smoking, and sleep duration between men and women. CONCLUSIONS The J-MICC Study collected lifestyle and clinical data and biospecimens from over 90,000 participants. This cohort is expected to be a valuable resource for the national and international scientific community in providing evidence to support longer healthy lives.
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Affiliation(s)
- Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine.,Department of Oral Epidemiology, Hiroshima University Graduate School of Biomedical and Health Sciences
| | - Sayo Kawai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine.,Department of Public Health, Aichi Medical University School of Medicine
| | - Mineko Tsukamoto
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Yuka Kadomatsu
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Yoko Kubo
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Mako Nagayoshi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine
| | - Tae Sasakabe
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine.,Department of Public Health, Aichi Medical University School of Medicine
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine
| | - Hidetaka Eguchi
- Diagnosis and Therapeutics of Intractable Diseases and Intractable Disease Research Center, Juntendo University Graduate School of Medicine
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences
| | - Hiroaki Ikezaki
- Department of Comprehensive General Internal Medicine, Kyushu University Graduate School, Faculty of Medical Sciences.,Department of General Internal Medicine, Kyushu University Hospital
| | - Masayuki Murata
- Department of General Internal Medicine, Kyushu University Hospital
| | - Norihiro Furusyo
- Department of Environmental Medicine and Infectious Diseases, Kyushu University Graduate School of Medical Sciences
| | - Keitaro Tanaka
- Department of Preventive Medicine, Faculty of Medicine, Saga University
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute.,Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute.,Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute
| | - Miho Kusakabe
- Cancer Prevention Center, Chiba Cancer Center Research Institute
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences
| | - Rie Ibusuki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences
| | - Ippei Shimoshikiryo
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences
| | - Takeshi Nishiyama
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine
| | - Etsuko Ozaki
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine
| | - Isao Watanabe
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine
| | - Kiyonori Kuriki
- Laboratory of Public Health, Division of Nutritional Sciences, School of Food and Nutritional Sciences, University of Shizuoka
| | | | - Hirotsugu Ueshima
- Center for Epidemiologic Research in Asia, Shiga University of Medical Science
| | - Kenji Matsui
- Division of Bioethics and Healthcare Law, The National Cancer Center Japan
| | - Kokichi Arisawa
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences
| | - Hirokazu Uemura
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences.,College of Nursing Art and Science, University of Hyogo
| | | | - Sho Nakamura
- Cancer Prevention and Control Division, Kanagawa Cancer Center Research Institute.,School of Health of Innovation, Kanagawa University of Human Services
| | - Hiroto Narimatsu
- Cancer Prevention and Control Division, Kanagawa Cancer Center Research Institute.,School of Health of Innovation, Kanagawa University of Human Services
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine
| | | | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine
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Kubo Y, Imaizumi T, Ando M, Nakatochi M, Yasuda Y, Honda H, Kuwatsuka Y, Kato S, Kikuchi K, Kondo T, Iwata M, Nakashima T, Yasui H, Takamatsu H, Okajima H, Yoshida Y, Maruyama S. Association between kidney function and genetic polymorphisms in atherosclerotic and chronic kidney diseases: A cross-sectional study in Japanese male workers. PLoS One 2017; 12:e0185476. [PMID: 29016630 PMCID: PMC5634546 DOI: 10.1371/journal.pone.0185476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022] Open
Abstract
Background Several single nucleotide polymorphisms (SNPs) have been implicated in the predisposition to chronic kidney disease (CKD). Atherosclerotic disease is deeply involved in the incidence of CKD; however, whether SNPs related to arteriosclerosis are involved in CKD remains unclear. This study aimed to identify SNPs associated with CKD and to examine whether risk allele accumulation is associated with CKD. Methods We conducted a cross-sectional study using data of 4814 male workers to examine the association between estimated glomerular filtration rate (eGFR) and 59 candidate polymorphisms (17 CKD, 42 atherosclerotic diseases). We defined the genetic risk score (GRS) as the total number of risk alleles that showed a significant association in this analysis and examined the relationship with CKD (eGFR < 60 ml/min/1.73m2). Multivariate logistic regression, discrimination by area under the receiver operating characteristic curve, integrated discrimination improvement (IDI), and category-free net reclassification improvement (cNRI) were evaluated. Results In total, 432 participants were categorized as having CKD. We found eight candidate SNPs with P value < 0.05 (CX3CR1 rs3732379, SHROOM3 rs17319721, MTP rs1800591, PIP5K1B rs4744712, APOA5 rs662799, BRAP rs3782886, SPATA5L1 rs2467853, and MCP1 rs1024611) in the multivariate linear regression adjusted for age, body mass index, systolic blood pressure, and fasting blood glucose. Among these eight SNPs, BRAP rs3782886 and SPATA5L1 rs2467853 were significantly associated with eGFR (false discovery rate < 0.05). GRS was significantly associated with CKD (odds ratio, 1.17; 95% confidence interval, 1.09–1.26). C-statisics improved from 0.775 to 0.780 but showed no statistical significance. However, adding GRS significantly improved IDI and cNRI (0.0057, P = 0.0028, and 0.212, P < 0.001, respectively). Conclusions After adjustment for clinical factors, kidney function was associated with BRAP rs3782886 and SPATA5L1 rs2467853 and the GRS for CKD that we developed was associated CKD.
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Affiliation(s)
- Yoko Kubo
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Takahiro Imaizumi
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiko Ando
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
- * E-mail:
| | - Masahiro Nakatochi
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Yoshinari Yasuda
- Department of CKD Initiatives, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Yachiyo Kuwatsuka
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Sawako Kato
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyoko Kikuchi
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Kondo
- Program in Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masamitsu Iwata
- Safety and Health Promotion Division, Toyota Motor Corporation, Toyota, Japan
| | - Toru Nakashima
- Safety and Health Promotion Division, Toyota Motor Corporation, Toyota, Japan
| | - Hiroshi Yasui
- Safety and Health Promotion Division, Toyota Motor Corporation, Toyota, Japan
| | - Hideki Takamatsu
- R & D Management Division, Toyota Motor Corporation, Toyota, Japan
| | - Hiroshi Okajima
- R & D Management Division, Toyota Motor Corporation, Toyota, Japan
| | - Yasuko Yoshida
- Innovative Research Center for Preventative Medical Engineering, Nagoya University, Nagoya, Japan
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Appropriate LDL-C-to-HDL-C Ratio Cutoffs for Categorization of Cardiovascular Disease Risk Factors among Uygur Adults in Xinjiang, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:235. [PMID: 26907312 PMCID: PMC4772255 DOI: 10.3390/ijerph13020235] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 02/02/2016] [Accepted: 02/14/2016] [Indexed: 01/21/2023]
Abstract
Elevated LDL-C/HDL-C ratio has been shown to be a marker of lipid metabolism as well as a good predictor of coronary artery disease (CAD). Thus, the aim of this study was to investigate whether the LDL-C/HDL-C ratio is useful for detecting cardiovascular disease (CVD) risk factors in general healthy Uygur adults in Xinjiang. A total of 4047 Uygur subjects aged ≥35 years were selected from the Cardiovascular Risk Survey (CRS) study which was carried out from October 2007 to March 2010. Anthropometric data, blood pressure, lipid profile and fasting glucose were measured in all participants. The prevalence, sensitivity, specificity and distance on the receiver operating characteristic (ROC) curve of each LDL-C/HDL-C ratio were calculated. The prevalence of high LDL-C and low HDL-C cholesterol was high and positively correlated with higher LDL-C/HDL-C ratio in the Uygur population. In both men and women, we detected a slight apparent trend of high prevalence of hypertension and hypercholesterolemia with higher LDL-C/HDL-C ratio. Our study also demonstrated that the discriminatory power of the LDL-C/HDL-C ratio for CVD risk factors was slightly stronger in men than in women. Analysis of the shortest distance in the ROC curves for hypertension, dyslipidemia, diabetes, or ≥two of these risk factors suggested a LDL-C/HDL-C ratio cutoff of 2.5 for both men and women. The results of this study showed that a LDL-C/HDL-C ratio cut-off of 2.5 might be used as the predictive marker to detect CVD risk factors among Uygur adults in Xinjiang.
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