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Satny M, Todorovova V, Altschmiedova T, Hubacek JA, Dlouha L, Lanska V, Soska V, Kyselak O, Freiberger T, Bobak M, Vrablik M. Genetic risk score in patients with the APOE2/E2 genotype as a predictor of familial dysbetalipoproteinemia. J Clin Lipidol 2024; 18:e230-e237. [PMID: 38044203 DOI: 10.1016/j.jacl.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND Familial dysbetalipoproteinemia (FD) is an autosomal recessive (rarely dominant) inherited disorder that is almost exclusively associated with the apolipoprotein E gene (APOE) variability. Nonetheless, only a small proportion of APOE2/E2 subjects develop the phenotype for mixed dyslipidemia; the context of other trigger metabolic or genetic factors remains unknown. METHODS One hundred and one patients with FD and eighty controls (all APOE2/E2 homozygotes; rs429358) were screened for 18 single-nucleotide polymorphisms (SNPs) within the genes involved in triglyceride metabolism. RESULTS Two SNPs were significantly associated with the FD phenotype (rs439401 within APOE; P < 0.0005 and rs964184 within ZPR1/APOA5/A4/C3/A1 gene cluster; P < 0.0001). Unweighted genetic risk scores - from these two SNPs (GRS2), and, also, additional 13 SNPs with P-value below 0.9 (GRS15) - were created as an additional tool to improve the risk estimation of FD development in subjects with the APOE2/E2 genotype. Both GRS2 and GRS15 were significantly (P < 0.0001) increased in patients and both GRSs discriminated almost identically between the groups (P = 0.86). Subjects with an unweighted GRS2 of three or more had an almost four-fold higher risk of FD development than other individuals (odds ratio (OR) 3.58, 95% confidence interva (CI): 1.78-7.18, P < 0.0005). CONCLUSIONS We identified several SNPs that are individual additive factors influencing FD development. The use of unweighted GRS2 is a simple and clinically relevant tool that further improves the prediction of FD in APOE2/E2 homozygotes with corresponding biochemical characteristics.
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Affiliation(s)
- Martin Satny
- 3rd Department of Internal Medicine, First Faculty of Medicine Charles University, General University Hospital, Prague, Czech Republic (Drs Satny, Todorovova, Altschmiedova, Hubacek and Vrablik).
| | - Veronika Todorovova
- 3rd Department of Internal Medicine, First Faculty of Medicine Charles University, General University Hospital, Prague, Czech Republic (Drs Satny, Todorovova, Altschmiedova, Hubacek and Vrablik)
| | - Tereza Altschmiedova
- 3rd Department of Internal Medicine, First Faculty of Medicine Charles University, General University Hospital, Prague, Czech Republic (Drs Satny, Todorovova, Altschmiedova, Hubacek and Vrablik)
| | - Jaroslav A Hubacek
- 3rd Department of Internal Medicine, First Faculty of Medicine Charles University, General University Hospital, Prague, Czech Republic (Drs Satny, Todorovova, Altschmiedova, Hubacek and Vrablik); Centre of Experimental Medicine, Institute of Clinical and Experimental Medicine, Prague, Czech Republic (Drs Hubacek and Lanska)
| | - Lucie Dlouha
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic (Dr Dlouha)
| | - Vera Lanska
- Centre of Experimental Medicine, Institute of Clinical and Experimental Medicine, Prague, Czech Republic (Drs Hubacek and Lanska)
| | - Vladimir Soska
- Clinical Biochemistry Department, St. Anne University Hospital, Brno, Czech Republic (Drs Soska and Kyselak); 2nd Internal Department, Faculty of Medicine Masaryk University and St. Anne University Hospital, Brno, Czech Republic (Drs Soska and Kyselak)
| | - Ondrej Kyselak
- Clinical Biochemistry Department, St. Anne University Hospital, Brno, Czech Republic (Drs Soska and Kyselak); 2nd Internal Department, Faculty of Medicine Masaryk University and St. Anne University Hospital, Brno, Czech Republic (Drs Soska and Kyselak)
| | - Tomas Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, and Medical Faculty, Masaryk University, Brno, Czech Republic (Dr Freiberger)
| | - Martin Bobak
- Institute of Epidemiology and Health Care, University College London, London WC1E 7HB, United Kingdom, and Medical Faculty, Masaryk University, Brno, Czech Republic (Dr Bobak)
| | - Michal Vrablik
- 3rd Department of Internal Medicine, First Faculty of Medicine Charles University, General University Hospital, Prague, Czech Republic (Drs Satny, Todorovova, Altschmiedova, Hubacek and Vrablik)
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Walia GK, Panniyammakal J, Agarwal T, Jalal R, Gupta R, Ramakrishnan L, Tandon N, Roy A, Krishnan A, Prabhakaran D. Evaluation of genetic variants related to lipid levels among the North Indian population. Front Genet 2024; 14:1234693. [PMID: 38348409 PMCID: PMC10859749 DOI: 10.3389/fgene.2023.1234693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/31/2023] [Indexed: 02/15/2024] Open
Abstract
Background: A heavy burden of cardiometabolic conditions on low- and middle-income countries like India that are rapidly undergoing urbanization remains unaddressed. Indians are known to have high levels of triglycerides and low levels of HDL-C along with moderately higher levels of LDL-C. The genome-wide findings from Western populations need to be validated in an Indian context for a better understanding of the underlying etiology of dyslipidemia in India. Objective: We aim to validate 12 genetic variants associated with lipid levels among rural and urban Indian populations and derive unweighted and weighted genetic risk scores (uGRS and wGRS) for lipid levels among the Indian population. Methods: Assuming an additive model of inheritance, linear regression models adjusted for all the possible covariates were run to examine the association between 12 genetic variants and total cholesterol, triglycerides, HDL-C, LDL-C, and VLDL-C among 2,117 rural and urban Indian participants. The combined effect of validated loci was estimated by allelic risk scores, unweighted and weighted by their effect sizes. Results: The wGRS for triglycerides and VLDL-C was derived based on five associated variants (rs174546 at FADS1, rs17482753 at LPL, rs2293889 at TRPS1, rs4148005 at ABCA8, and rs4420638 at APOC1), which was associated with 36.31 mg/dL of elevated triglyceride and VLDL-C levels (β = 0.95, SE = 0.16, p < 0.001). Similarly, every unit of combined risk score (rs2293889 at TRPS1 and rs4147536 at ADH1B) was associated with 40.62 mg/dL of higher total cholesterol (β = 1.01, SE = 0.23, p < 0.001) and 33.97 mg/dL of higher LDL-C (β = 1.03, SE = 0.19, p < 0.001) based on its wGRS (rs2293889 at TRPS1, rs4147536 at ADH1B, rs4420638 at APOC1, and rs660240 at CELSR2). The wGRS derived from five associated variants (rs174546 at FADS1, rs17482753 at LPL, rs4148005 at ABCA8, rs4420638 at APOC1, and rs7832643 at PLEC) was associated with 10.64 mg/dL of lower HDL-C (β = -0.87, SE = 0.14, p < 0.001). Conclusion: We confirm the role of eight genome-wide association study (GWAS) loci related to different lipid levels in the Indian population and demonstrate the combined effect of variants for lipid traits among Indians by deriving the polygenic risk scores. Similar studies among different populations are required to validate the GWAS loci and effect modification of these loci by lifestyle and environmental factors related to urbanization.
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Affiliation(s)
- Gagandeep Kaur Walia
- Public Health Foundation of India, New Delhi, India
- Centre for Chronic Disease Control, New Delhi, India
| | - Jeemon Panniyammakal
- Centre for Chronic Disease Control, New Delhi, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Tripti Agarwal
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Ruchita Jalal
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Ruby Gupta
- Centre for Chronic Disease Control, New Delhi, India
| | | | - Nikhil Tandon
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Ambuj Roy
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Anand Krishnan
- Indian Institute of Public Health-Delhi, New Delhi, India
| | - Dorairaj Prabhakaran
- Public Health Foundation of India, New Delhi, India
- Centre for Chronic Disease Control, New Delhi, India
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Radhika A, Burgula S, Badapanda C, Hussain T, Naushad SM. Elucidation of genetic determinants of dyslipidaemia using a global screening array for the early detection of coronary artery disease. Mamm Genome 2023; 34:632-643. [PMID: 37668737 DOI: 10.1007/s00335-023-10017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023]
Abstract
Dyslipidemia is a major risk factor for the development of coronary artery disease (CAD). Understanding the genetic determinants of dyslipidemia can provide valuable information on the pathogenesis of CAD and aid in the development of early detection strategies. In this study, we used a Global Screening Array (GSA) to elucidate the genetic factors associated with dyslipidemia and their potential role in the prediction of CAD. We conducted a GSA-based association study in 265 subjects to identify the genetic loci associated with dyslipidemia traits using Multiple Linear Regression (MLR) and Logistic Regression (LR), Classification and Regression Tree (CART), and Manhattan plots. We identified an association between dyslipidemia and variants identified in genes such as JCAD, GLIS3, CD38, FN1, CELSR2, MTNR1B, GIPR, DYM, APOB, APOE, ADCY5. The MLR models explained 62%, 71%, and 81% of the variability in HDL, LDL, and triglycerides, respectively. The Area Under the Curve (AUC) values in the LR models of HDL, LDL, and triglycerides were 1.00, 0.94, and 0.95, respectively. CART models identified novel gene-gene interactions influencing the risk for dyslipidemia. To conclude, we have identified the association of 12 SNVs with dyslipidemia and demonstrated their clinical utility in four different models such as MLR, LR, CART, and Manhattan plots. The identified genetic variants and associated pathways shed light on the underlying biology of dyslipidemia and offer potential avenues for precision medicine strategies in the management of CAD.
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Affiliation(s)
- Ananthaneni Radhika
- Genomics Division, Yoda Lifeline Diagnostics Pvt Ltd, 6-3-862/A, Lal Bungalow Add On, Ameerpet, Hyderabad, 500016, India
- Department of Microbiology, Osmania University, Taranaka, Hyderabad, 500007, India
| | - Sandeepta Burgula
- Department of Microbiology, Osmania University, Taranaka, Hyderabad, 500007, India.
| | - Chandan Badapanda
- Genomics Division, Yoda Lifeline Diagnostics Pvt Ltd, 6-3-862/A, Lal Bungalow Add On, Ameerpet, Hyderabad, 500016, India
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Shaik Mohammad Naushad
- Genomics Division, Yoda Lifeline Diagnostics Pvt Ltd, 6-3-862/A, Lal Bungalow Add On, Ameerpet, Hyderabad, 500016, India.
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Huang QQ, Sallah N, Dunca D, Trivedi B, Hunt KA, Hodgson S, Lambert SA, Arciero E, Wright J, Griffiths C, Trembath RC, Hemingway H, Inouye M, Finer S, van Heel DA, Lumbers RT, Martin HC, Kuchenbaecker K. Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistani and Bangladeshi individuals. Nat Commun 2022; 13:4664. [PMID: 35945198 PMCID: PMC9363492 DOI: 10.1038/s41467-022-32095-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/15/2022] [Indexed: 12/30/2022] Open
Abstract
Individuals with South Asian ancestry have a higher risk of heart disease than other groups but have been largely excluded from genetic research. Using data from 22,000 British Pakistani and Bangladeshi individuals with linked electronic health records from the Genes & Health cohort, we conducted genome-wide association studies of coronary artery disease and its key risk factors. Using power-adjusted transferability ratios, we found evidence for transferability for the majority of cardiometabolic loci powered to replicate. The performance of polygenic scores was high for lipids and blood pressure, but lower for BMI and coronary artery disease. Adding a polygenic score for coronary artery disease to clinical risk factors showed significant improvement in reclassification. In Mendelian randomisation using transferable loci as instruments, our findings were consistent with results in European-ancestry individuals. Taken together, trait-specific transferability of trait loci between populations is an important consideration with implications for risk prediction and causal inference.
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Affiliation(s)
- Qin Qin Huang
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Neneh Sallah
- Institute of Health Informatics, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Diana Dunca
- Institute of Health Informatics, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Bhavi Trivedi
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Karen A Hunt
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sam Hodgson
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Elena Arciero
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals National Health Service (NHS) Foundation Trust, Bradford, UK
| | - Chris Griffiths
- Institute of Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard C Trembath
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Harry Hemingway
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, University College London, London, UK
- University College London Hospitals Biomedical Research Centre (UCLH BRC), London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Sarah Finer
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - R Thomas Lumbers
- Institute of Health Informatics, University College London, London, UK
- University College London Hospitals Biomedical Research Centre (UCLH BRC), London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
| | - Hilary C Martin
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Karoline Kuchenbaecker
- UCL Genetics Institute, University College London, London, UK.
- Division of Psychiatry, University College London, London, UK.
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Lee HS, Kim B, Park T. Transethnic meta-analysis of exome-wide variants identifies new loci associated with male-specific metabolic syndrome. Genes Genomics 2022; 44:629-636. [PMID: 35384631 DOI: 10.1007/s13258-021-01214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/29/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Metabolic syndrome (MetS) is a group of very common human conditions promoting strong understand the impact of rare variants, beyond exome-wide association studies, to potentially discover causative variants, across different ethnic populations. OBJECTIVE We performed transethnic, exome-wide MetS association studies on MetS in men. METHODS We analyzed genotype data of 5302 European subjects (2658 cases and 2644 controls), in the discovery stage of the European METabolic Syndrome In Men study, generated from exome chips, and 2481 subjects (714 cases and 1767 controls), in the replication stage, across 6 independent cohorts of 5 ancestries (T2D-GENES consortium), using whole-exome sequencing. We therefore evaluated gene-level and variant-level associations, of rare variants for MetS, using logistic regression (LR) and multivariate analyses (MulA). RESULTS Gene-based association found the gene for the cholesteryl ester transfer protein (CETP) (from MulA, p value = 4.67 × 10-9; from LR, p value = 0.009) to well associate with MetS. At two missense variants, from 8 rare variants in CETP, Ala390Pro (rs5880) (from MulA, p value = 1.28 × 10-7; from LR, p value = 1.34 × 10-4) and Arg468Gln (rs1800777) (from MulA, p value = 2.40 × 10-5; from LR, p value = 1.49 × 10-3) significantly associated with MetS across five ancestries. CONCLUSIONS Our findings highlight novel rare variants of genes that confer MetS susceptibility, in Europeans, that are shared with diverse populations, emphasizing an opportunity to further understand the biological target or genes that underlie MetS, across populations.
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Affiliation(s)
- Ho-Sun Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Daegu Institution, National Forensic Service, 33-14, Hogukro, Waegwon-eup, Chilgok-gun, Gyeomgsamgbuk-do, Republic of Korea
| | - Boram Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Statistics, Seoul National University, Seoul, 08826, Republic of Korea.
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Gorre M, Rayabarapu P, Battini SR, Irgam K, Battini MR. Analysis of 61 SNPs from the CAD specific genomic loci reveals unique set of SNPs as significant markers in the Southern Indian population of Hyderabad. BMC Cardiovasc Disord 2022; 22:148. [PMID: 35379196 PMCID: PMC8981708 DOI: 10.1186/s12872-022-02562-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Background The present study is a part of the major project on coronary artery disease (CAD) carried out at Indian Statistical Institute, Hyderabad to investigate the pattern of association of SNPs selected from the CAD specific genomic loci. The study is expected to portray the genetic susceptibility profile of CAD specifically in the Southern Indian population of Hyderabad. Methods The study was conducted in a cohort of 830 subjects comprising 350 CAD cases and 480 controls from Hyderabad. A prioritized set of 61 SNPs selected from the NHGRI GWAS catalogue were genotyped using FluidigmNanofluidic SNP Genotyping System and appropriate statistical analyses were used in interpreting the results. Results After data pruning, out of 45 SNPs qualified for the association analysis, four SNPs were found to be highly significantly associated with increased risk for CAD even after Bonferroni correction for multiple testing (p < 0.001). These results were also replicated in the random subsets of the pooled cohort (70, 50 and 30%) suggesting internal consistency. The ROC analysis of the risk scores of the significant SNPs suggested highly significant area under curve (AUC = 0.749; p < 0.0001) implying predictive utility of these risk variants. Conclusions The rs10455872 of LP(A) gene in particular showed profound risk for CAD (OR 35.9; CI 16.7–77.2) in this regional Indian population. The other significant SNP associations observed with respect to the pooled CAD cohort and in different anatomical and phenotypic severity categories reflected on the role of genetic heterogeneity in the clinical heterogeneity of CAD. The SNP rs7582720 of WDR12 gene, albeit not individually associated with CAD, was found to be conferring significant risk through epistatic interaction with two SNPs (rs6589566, rs1263163 in ZPR1, APOA5-APOA4 genes) of the 11q23.3 region. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-022-02562-4.
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Affiliation(s)
- Manjula Gorre
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, 500007, India
| | | | - Sriteja Reddy Battini
- Dr Pinnamaneni Siddhartha Institute of Medical Sciences and Research Foundation, Vijayawada, India
| | - Kumuda Irgam
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, 500007, India
| | - Mohan Reddy Battini
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, 500007, India. .,Molecular Anthropology Laboratory, Indian Statistical Institute, Hyderabad, India.
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Rout M, Lerner M, Blackett PR, Peyton MD, Stavrakis S, Sidorov E, Sanghera DK. Ethnic differences in ApoC-III concentration and the risk of cardiovascular disease: No evidence for the cardioprotective role of rare/loss of function APOC3 variants in non-Europeans. AMERICAN HEART JOURNAL PLUS : CARDIOLOGY RESEARCH AND PRACTICE 2022; 13:100128. [PMID: 35528316 PMCID: PMC9075110 DOI: 10.1016/j.ahjo.2022.100128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Hypertriglyceridemia is as an independent risk factor for cardiovascular disease (CVD). Apolipoprotein C-III (ApoC-III) is known to regulate triglyceride (TG) metabolism. However, the causal association between ApoC-III and CVD development is unclear. The objectives were to examine the impact of ApoC-III concentration on TG and lipoproteins and investigate the role of known rare loss-of-function APOC3 variants for modulating ApoC-III, TG concentrations and CVD risk in different ethnic groups. METHODS Plasma ApoC-III levels were measured in a multiethnic sample of 518 individuals comprising 271 Asian Indians (Sikhs), 87 Caucasians, 80 African Americans, and 80 Hispanics. RESULTS ApoC-III levels showed a robust association with TG in Asian Indians (r = 0.5, p = 1.1 × 10-23), Caucasians (r = 0.4, p = 7.2 × 10-4), and Hispanics (r = 0.9, p = 2.7x × 10-28). African Americans had lowest ApoC-III and TG concentrations and highest (44%) prevalence of coronary artery disease (CAD). ApoC-III levels correlated with fasting blood glucose (r = 0.25, p = 6.1 × 10-5) in Asian Indians and central adiposity in Hispanics (waist: r = 0.22, p = 0.05; waist-hip ratio: r = 0.24, p = 0.04). The carriers of rare variants IVS1-2G-A (rs373975305); A43T (rs147210663) and IVS3 + 1G-T (rs140621530) showed high TG but not low ApoC-III levels in Asian Indians and Caucasians. CONCLUSION These results highlight the challenges of generalizing antisense ApoC-III inhibition for treating atherosclerotic disease in dyslipidemia that may benefit only specific sub-populations. The observed ethnic differences in ApoC-III concentrations and CAD risk factors, emphasize in-depth genetic and metabolomics evaluations on diverse ancestries.
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Affiliation(s)
- Madhusmita Rout
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Megan Lerner
- Department of Surgery, Oklahoma University of Health Sciences Center, Oklahoma City, OK, USA
| | - Piers R. Blackett
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Marvin D. Peyton
- Department of Surgery, Oklahoma University of Health Sciences Center, Oklahoma City, OK, USA
| | - Stavros Stavrakis
- Department of Cardiology, Oklahoma University of Health Sciences Center, Oklahoma City, OK, USA
| | - Evgeny Sidorov
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S.L Young Blvd #2040, 73104 Oklahoma City, OK, USA
| | - Dharambir K. Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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Goyal S, Tanigawa Y, Zhang W, Chai JF, Almeida M, Sim X, Lerner M, Chainakul J, Ramiu JG, Seraphin C, Apple B, Vaughan A, Muniu J, Peralta J, Lehman DM, Ralhan S, Wander GS, Singh JR, Mehra NK, Sidorov E, Peyton MD, Blackett PR, Curran JE, Tai ES, van Dam R, Cheng CY, Duggirala R, Blangero J, Chambers JC, Sabanayagam C, Kooner JS, Rivas MA, Aston CE, Sanghera DK. APOC3 genetic variation, serum triglycerides, and risk of coronary artery disease in Asian Indians, Europeans, and other ethnic groups. Lipids Health Dis 2021; 20:113. [PMID: 34548093 PMCID: PMC8456544 DOI: 10.1186/s12944-021-01531-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Hypertriglyceridemia has emerged as a critical coronary artery disease (CAD) risk factor. Rare loss-of-function (LoF) variants in apolipoprotein C-III have been reported to reduce triglycerides (TG) and are cardioprotective in American Indians and Europeans. However, there is a lack of data in other Europeans and non-Europeans. Also, whether genetically increased plasma TG due to ApoC-III is causally associated with increased CAD risk is still unclear and inconsistent. The objectives of this study were to verify the cardioprotective role of earlier reported six LoF variants of APOC3 in South Asians and other multi-ethnic cohorts and to evaluate the causal association of TG raising common variants for increasing CAD risk. METHODS We performed gene-centric and Mendelian randomization analyses and evaluated the role of genetic variation encompassing APOC3 for affecting circulating TG and the risk for developing CAD. RESULTS One rare LoF variant (rs138326449) with a 37% reduction in TG was associated with lowered risk for CAD in Europeans (p = 0.007), but we could not confirm this association in Asian Indians (p = 0.641). Our data could not validate the cardioprotective role of other five LoF variants analysed. A common variant rs5128 in the APOC3 was strongly associated with elevated TG levels showing a p-value 2.8 × 10- 424. Measures of plasma ApoC-III in a small subset of Sikhs revealed a 37% increase in ApoC-III concentrations among homozygous mutant carriers than the wild-type carriers of rs5128. A genetically instrumented per 1SD increment of plasma TG level of 15 mg/dL would cause a mild increase (3%) in the risk for CAD (p = 0.042). CONCLUSIONS Our results highlight the challenges of inclusion of rare variant information in clinical risk assessment and the generalizability of implementation of ApoC-III inhibition for treating atherosclerotic disease. More studies would be needed to confirm whether genetically raised TG and ApoC-III concentrations would increase CAD risk.
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Affiliation(s)
- Shiwali Goyal
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore , 117549, Singapore
| | - Marcio Almeida
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore , 117549, Singapore
| | - Megan Lerner
- Department of Surgery, Oklahoma University of Health Sciences Center, Oklahoma City, OK, USA
| | - Juliane Chainakul
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S. L Young Blvd #2040, Oklahoma City, OK, 73104, USA
| | - Jonathan Garcia Ramiu
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S. L Young Blvd #2040, Oklahoma City, OK, 73104, USA
| | - Chanel Seraphin
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S. L Young Blvd #2040, Oklahoma City, OK, 73104, USA
| | - Blair Apple
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S. L Young Blvd #2040, Oklahoma City, OK, 73104, USA
| | - April Vaughan
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S. L Young Blvd #2040, Oklahoma City, OK, 73104, USA
| | - James Muniu
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA
| | - Juan Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Donna M Lehman
- Departments of Medicine and Epidemiology and Biostatistics, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Sarju Ralhan
- Hero DMC Heart Institute, Ludhiana, Punjab, India
| | | | - Jai Rup Singh
- Central University of Punjab, Bathinda, Punjab, India
| | - Narinder K Mehra
- All India Institute of Medical Sciences and Research, New Delhi, India
| | - Evgeny Sidorov
- Department of Neurology, University of Oklahoma Health Sciences Center, 920 S. L Young Blvd #2040, Oklahoma City, OK, 73104, USA
| | - Marvin D Peyton
- Department of Surgery, Oklahoma University of Health Sciences Center, Oklahoma City, OK, USA
| | - Piers R Blackett
- Department of Pediatrics, Section of Endocrinology, Oklahoma University of Health Sciences Center, Oklahoma City, OK, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore , 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, Singapore , 119228, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Rob van Dam
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, Singapore , 119228, Singapore
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ching-Yu Cheng
- Duke-NUS Medical School, Singapore, 169857, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751, Singapore
- National University of Singapore, Singapore, 119077, Singapore
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Lee Kong Chan School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Charumathi Sabanayagam
- Duke-NUS Medical School, Singapore, 169857, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
| | - Manuel A Rivas
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Christopher E Aston
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA
| | - Dharambir K Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA.
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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9
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Masjoudi S, Sedaghati-Khayat B, Givi NJ, Bonab LNH, Azizi F, Daneshpour MS. Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study. Sci Rep 2021; 11:10305. [PMID: 33986338 PMCID: PMC8119714 DOI: 10.1038/s41598-021-89509-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
Metabolic syndrome (MetS) is one of the most important risk factors for cardiovascular disease. The 11p23.3 chromosomal region plays a potential role in the pathogenesis of MetS. The present study aimed to assess the association between 18 single nucleotide polymorphisms (SNPs) located at the BUD13, ZPR1, and APOA5 genes with MetS in the Tehran Cardio-metabolic Genetics Study (TCGS). In 5421 MetS affected and non-affected participants, we analyzed the data using two models. The first model (MetS model) examined SNPs' association with MetS. The second model (HTg-MetS Model) examined the association of SNPs with MetS affection participants who had a high plasma triglyceride (TG). The four-gamete rules were used to make SNP sets from correlated nearby SNPs. The kernel machine regression models and single SNP regression evaluated the association between SNP sets and MetS. The kernel machine results showed two sets over three sets of correlated SNPs have a significant joint effect on both models (p < 0.0001). Also, single SNP regression results showed that the odds ratios (ORs) for both models are almost similar; however, the p-values had slightly higher significance levels in the HTg-MetS model. The strongest ORs in the HTg-MetS model belonged to the G allele in rs2266788 (MetS: OR = 1.3, p = 3.6 × 10–7; HTg-MetS: OR = 1.4, p = 2.3 × 10–11) and the T allele in rs651821 (MetS: OR = 1.3, p = 2.8 × 10–7; HTg-MetS: OR = 1.4, p = 3.6 × 10–11). In the present study, the kernel machine regression models could help assess the association between the BUD13, ZPR1, and APOA5 gene variants (11p23.3 region) with lipid-related traits in MetS and MetS affected with high TG.
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Affiliation(s)
- Sajedeh Masjoudi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, PO Box 19195-4763, Tehran, Iran
| | - Bahareh Sedaghati-Khayat
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, PO Box 19195-4763, Tehran, Iran
| | - Niloufar Javanrouh Givi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, PO Box 19195-4763, Tehran, Iran
| | - Leila Najd Hassan Bonab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, PO Box 19195-4763, Tehran, Iran
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam S Daneshpour
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, PO Box 19195-4763, Tehran, Iran.
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10
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The rs599839 A>G Variant Disentangles Cardiovascular Risk and Hepatocellular Carcinoma in NAFLD Patients. Cancers (Basel) 2021; 13:cancers13081783. [PMID: 33917919 PMCID: PMC8068289 DOI: 10.3390/cancers13081783] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Dyslipidemia is a hallmark of nonalcoholic fatty liver disease (NAFLD) and the rs599839 variant in the CELSR2-PSRC1-SORT1 genetic cluster, has been associated with a protection against cardiovascular events. Here, we revealed a novel link between the rs599839 variant and hepatocellular carcinoma (HCC) whose onset in the context of NAFLD is rapidly increasing. We found that the rs599839 variant disentangled the risk of HCC from that of cardiovascular abnormalities by modulating SORT1 and PSRC1 expressions. The latter emerged as a potential modifier of liver carcinogenesis. Abstract Background and Aims: Dyslipidemia and cardiovascular diseases (CVD) are comorbidities of nonalcoholic fatty liver disease (NAFLD), which ranges from steatosis to hepatocellular carcinoma (HCC). The rs599839 A>G variant, in the CELSR2-PSRC1-SORT1 gene cluster, has been associated CVD, but its impact on metabolic traits and on the severity liver damage in NAFLD has not been investigated yet. Methods: We evaluated the effect of the rs599839 variant in 1426 NAFLD patients (Overall cohort) of whom 131 had HCC (NAFLD-HCC), in 500,000 individuals from the UK Biobank Cohort (UKBBC), and in 366 HCC samples from The Cancer Genome Atlas (TCGA). Hepatic PSRC1, SORT1 and CELSR2 expressions were evaluated by RNAseq (n = 125). Results: The rs599839 variant was associated with reduced circulating LDL, carotid intima-media thickness, carotid plaques and hypertension (p < 0.05) in NAFLD patients and with protection against dyslipidemia in UKBBC. The minor G allele was associated with higher risk of HCC, independently of fibrosis severity (odds ratio (OR): 5.62; 95% c.i. 1.77–17.84, p = 0.003), poor prognosis and advanced tumor stage (p < 0.05) in the overall cohort. Hepatic PSRC1, SORT1 and CELSR2 expressions were increased in NAFLD patients carrying the rs599839 variant (p < 0.0001). SORT1 mRNA levels negatively correlated with circulating lipids and with those of genes involved in lipoprotein turnover (p < 0.0001). Conversely, PSRC1 expression was positively related to that of genes implicated in cell proliferation (p < 0.0001). In TCGA, PSRC1 over-expression promoted more aggressive HCC development (p < 0.05). Conclusions: In sum, the rs599839 A>G variant is associated with protection against dyslipidemia and CVD in NAFLD patients, but as one it might promote HCC development by modulating SORT1 and PSRC1 expressions which impact on lipid metabolism and cell proliferation, respectively.
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11
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Esteve-Luque V, Padró-Miquel A, Fanlo-Maresma M, Corbella E, Corbella X, Pintó X, Candás-Estébanez B. Implication between Genetic Variants from APOA5 and ZPR1 and NAFLD Severity in Patients with Hypertriglyceridemia. Nutrients 2021; 13:nu13020552. [PMID: 33567543 PMCID: PMC7914661 DOI: 10.3390/nu13020552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Lipid metabolism disorders, especially hypertriglyceridemia (HTG), are risk factors for non-alcoholic fatty liver disease (NAFLD). However, the association between genetic factors related to HTG and the risk of NAFLD has been scarcely studied. Methods: A total of 185 subjects with moderate HTG were prospectively included. We investigated the association between genetic factors’ (five allelic variants with polygenic hypertriglyceridemia) clinical and biochemical biomarkers with NAFLD severity. The five allelic variants’ related clinical and biochemical data of HTG were studied in all the subjects. NAFLD was assessed by abdominal ultrasound and patients were divided into two groups, one with no or mild NAFLD and another with moderate/severe NAFLD. Results: Patients with moderate/severe NAFLD had higher weight and waist values and a higher prevalence of insulin resistance than patients with no or mild NAFLD. Moderate/severe NAFLD was independently associated with APOA5 rs3134406 and ZPR1 rs964184 variants, and also showed a significant inverse relationship with lipoprotein(a) [Lp(a)] concentrations. Conclusions: APOA5 rs3135506 and ZPR1 rs964184 variants and lipoprotein(a) are associated with moderate/severe NAFLD. This association was independent of body weight, insulin resistance, and other factors related to NAFLD.
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Affiliation(s)
- Virginia Esteve-Luque
- Cardiovascular Risk Unit, Internal Medicine Department, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (V.E.-L.); (M.F.-M.); (E.C.); (X.C.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- Medicine and Translational Research, University of Medicine, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Ariadna Padró-Miquel
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- Clinical Laboratory, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain
- CIBEROBN Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Marta Fanlo-Maresma
- Cardiovascular Risk Unit, Internal Medicine Department, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (V.E.-L.); (M.F.-M.); (E.C.); (X.C.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- Medicine and Translational Research, University of Medicine, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Emili Corbella
- Cardiovascular Risk Unit, Internal Medicine Department, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (V.E.-L.); (M.F.-M.); (E.C.); (X.C.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- CIBEROBN Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Xavier Corbella
- Cardiovascular Risk Unit, Internal Medicine Department, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (V.E.-L.); (M.F.-M.); (E.C.); (X.C.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- School of Medicine, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Xavier Pintó
- Cardiovascular Risk Unit, Internal Medicine Department, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (V.E.-L.); (M.F.-M.); (E.C.); (X.C.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- CIBEROBN Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- School of Medicine, Universitat de Barcelona, 08907 Barcelona, Spain
- Correspondence:
| | - Beatriz Candás-Estébanez
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (A.P.-M.); (B.C.-E.)
- Clinical Laboratory, Hospital Universitari de Bellvitge, 08907 L’Hospitalet de Llobregat, Spain
- CIBEROBN Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Clinical Biochemistry, SCIAS-Hospital de Barcelona, 08034 Barcelona, Spain
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12
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Goyal S, Sanghera DK. Genetic and Non-genetic Determinants of Cardiovascular Disease in South Asians. Curr Diabetes Rev 2021; 17:e011721190373. [PMID: 33461471 PMCID: PMC10370262 DOI: 10.2174/1573399817666210118103022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 01/09/2023]
Abstract
South Asians (SAs), people from the Indian subcontinent (e.g., India, Pakistan, Bangladesh, Sri Lanka, and Nepal) have a higher prevalence of cardiovascular disease (CVD) and suffer from a greater risk of CVD-associated mortality compared to other global populations. These problems are compounded by the alterations in lifestyles due to urbanization and changing cultural, social, economic, and political environments. Current methods of CV risk prediction are based on white populations that under-estimate the CVD risk in SAs. Prospective studies are required to obtain actual CVD morbidity/mortality rates so that comparisons between predicted CVD risk can be made with actual events. Overwhelming data support a strong influence of genetic factors. Genome-Wide Association Studies (GWAS) serve as a starting point for future genetic and functional studies since the mechanisms of action by which these associated loci influence CVD is still unclear. It is difficult to predict the potential implication of these findings in clinical settings. This review provides a systematic assessment of the risk factors, genetics, and environmental causes of CV health disparity in SAs, and highlights progress made in clinical and genomics discoveries in the rapidly evolving field, which has the potential to show clinical relevance in the near future.
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Affiliation(s)
- Shiwali Goyal
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Dharambir K Sanghera
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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13
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Manjula G, Pranavchand R, Kumuda I, Reddy BS, Reddy BM. The SNP rs7865618 of 9p21.3 locus emerges as the most promising marker of coronary artery disease in the southern Indian population. Sci Rep 2020; 10:21511. [PMID: 33298998 PMCID: PMC7726101 DOI: 10.1038/s41598-020-77080-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/05/2020] [Indexed: 11/09/2022] Open
Abstract
Development of coronary artery disease (CAD) is primarily due to the process of atherosclerosis, however the prognosis of CAD depends on pleiotropic effects of the genes located at 9p21.3 region. Genome wide association studies revealed association of variants in this region with CAD pathology. However, specific marker in predicting CAD development or progression is not yet identified. In the present study, 35 SNPs at 9p21.3 region, located in the cyclin dependent kinase inhibitor (CDKN2A/CDKN2B) genes, were genotyped among 350 CAD cases and 480 controls from the southern Indian population of Hyderabad using fluidigm nanofluidic SNP genotyping system and the data were analyzed using PLINK and R softwares. Of the 35 SNPs analysed, only one SNP, rs7865618, was found to be highly significantly associated with CAD, even after correction for multiple testing (p = 0.008). The AG and GG genotypes of this SNP conferred 3.08 and 1.93 folds increased risk for CAD respectively. In particular, this SNP was significantly associated with severe anatomic (triple vessel disease p = 0.023) and phenotypic (acute coronary syndrome p = 0.007) categories of CAD. Pair wise SNP interaction analysis between the SNPs of 9p21.3 and 11q23.3 regions revealed significantly increased risk of three SNPs of 11q23.3 region that were not associated individually, in conjunction with rs7865618 of 9p21.3.
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Affiliation(s)
- Gorre Manjula
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Irgam Kumuda
- Department of Genetics, Osmania University, Hyderabad, India
| | - B Sriteja Reddy
- Dr Pinnamaneni, Siddhartha Institute of Medical Sciences and Research Foundation, Vijayawada, India
| | - Battini Mohan Reddy
- Department of Genetics, Osmania University, Hyderabad, India. .,Molecular Anthropology Group, Indian Statistical Institute, Hyderabad, India. .,Emeritus Scientist (ICMR), Department of Genetics, Osmania University, Hyderabad, 500007, India.
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14
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Yang L, Ma L, Guo W, Fang Q, Lai X, Zhang X. Interaction of polymorphisms in APOA4-APOA5-ZPR1-BUD13 gene cluster and sleep duration on 5-year lipid changes in middle aged and older Chinese. Sleep 2020; 42:5513402. [PMID: 31181149 DOI: 10.1093/sleep/zsz115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/24/2019] [Indexed: 12/31/2022] Open
Abstract
STUDY OBJECTIVES Lipid profiles are influenced by both genetic and environmental factors. Genetic variants in the APOA4-APOA5-ZPR1-BUD13 gene cluster and aberrant sleep duration were independently identified to be associated with lipids in previous studies. We aimed to investigate whether sleep duration modified the genetic associations with longitudinal lipids changes. METHODS Four single nucleotide polymorphisms (SNPs), rs17119975, rs651821, rs7396835, and rs964184 in the APOA4-APOA5-ZPR1-BUD13 gene cluster were genotyped among 8648 apparently healthy subjects from the Dongfeng-Tongji (DFTJ) cohort. Information on sleep duration was obtained by questionnaires. Changes in total cholesterol, triglyceride, high-density lipoprotein cholesterol (HDL-c), low-density lipoprotein cholesterol (LDL-c), were evaluated from baseline to 5-year follow-up. RESULTS After multivariate adjustments, we found that rs651821 and weighted genetic risk score (GRS) were significantly associated with increased triglyceride, and the genetic association with triglyceride change consistently strengthened across sleep duration categories. The differences in triglyceride changes per increment of risk allele for rs651821 were 0.028 (SE = 0.017, p = 0.112), 0.051 (SE = 0.009, p < 0.001), and 0.064 (SE = 0.016, p < 0.001) in individuals with sleep duration ≤7, >7-<9, and ≥9 h, respectively (p interaction = 0.031). The GRS also showed a significant interaction with sleep duration categories for triglyceride change (p interaction = 0.010). In addition, all of the four SNPs and GRS were inversely related to HDL-c changes. CONCLUSIONS Longer sleep duration might exacerbate the adverse effects of SNPs in APOA4-APOA5-ZPR1-BUD13 gene cluster on 5-year triglyceride changes.
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Affiliation(s)
- Liangle Yang
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Ma
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenting Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Fang
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuefeng Lai
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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15
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Grubbs JJ, Lopes LE, van der Linden AM, Raizen DM. A salt-induced kinase is required for the metabolic regulation of sleep. PLoS Biol 2020; 18:e3000220. [PMID: 32315298 PMCID: PMC7173979 DOI: 10.1371/journal.pbio.3000220] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/20/2020] [Indexed: 12/16/2022] Open
Abstract
Many lines of evidence point to links between sleep regulation and energy homeostasis, but mechanisms underlying these connections are unknown. During Caenorhabditis elegans sleep, energetic stores are allocated to nonneural tasks with a resultant drop in the overall fat stores and energy charge. Mutants lacking KIN-29, the C. elegans homolog of a mammalian Salt-Inducible Kinase (SIK) that signals sleep pressure, have low ATP levels despite high-fat stores, indicating a defective response to cellular energy deficits. Liberating energy stores corrects adiposity and sleep defects of kin-29 mutants. kin-29 sleep and energy homeostasis roles map to a set of sensory neurons that act upstream of fat regulation as well as of central sleep-controlling neurons, suggesting hierarchical somatic/neural interactions regulating sleep and energy homeostasis. Genetic interaction between kin-29 and the histone deacetylase hda-4 coupled with subcellular localization studies indicate that KIN-29 acts in the nucleus to regulate sleep. We propose that KIN-29/SIK acts in nuclei of sensory neuroendocrine cells to transduce low cellular energy charge into the mobilization of energy stores, which in turn promotes sleep.
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Affiliation(s)
- Jeremy J. Grubbs
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lindsey E. Lopes
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - David M. Raizen
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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16
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Tantray JA, Reddy KP, Jamil K, Lone WG, Yerra SK. Genetic and Epigenetic Factors of E3/E3 Genotypes of APO-E Gene as a Strong Predictor for the Diagnosis of Coronary Artery Disease Patients of South India. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190724095158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The role of Apolipoprotein-E (APO-E) in lipid metabolism and cholesterol
transport is a key component of lipid metabolism which plays a role in diseases like hypercholesterolemia,
diabetes, and cardiovascular disease. The aim of this study was to determine the genotypes, allelic
frequencies, gene expression and methylation related to apolipoprotein E polymorphism in Coronary Artery
Disease (CAD) patients and compare with non-CAD healthy subjects of South Indian population.
Methods:
The APO-E alleles and genotypes were determined by PCR-RFLP. Gene expression profiles
for E3/E3 genotypes were determined using RT-PCR and methylation status was determined using
Methyl Specific PCR assay in one hundred patients and an equal number of controls.
Results:
Four APO-E genotypes (E4/E4, E3/E3, E3/E4, and E2/E3) were identified with different allele
frequency. Among these, E3/E3 genotype and E3 allele were found to be significantly higher in
cases than controls. The present study showed that the mRNA expression of APO-E was up-regulated
in CAD patients with E3/E3 genotype in comparison with controls. Methylation status indicated a significant
association of E3/E3 genotypes with the disease.
Conclusion:
Different populations studied worldwide showed inherent variable frequencies of the
APO-E alleles and genotypes, with the most frequent allele being E3. In this study, the APO-E genotypes
E2/E3/E4 showed variable response to CAD, further, there was a significant association of E3/E3
genotypes to CAD risk; this genotype can be suggested for the diagnosis of CAD.
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Affiliation(s)
| | | | - Kaiser Jamil
- Department of Genetics, Bhagwan Mahavir Medical Research Centre, 10-1-1, Mahavir Marg, Hyderabad-500004, Telangana, India
| | - Waseem Gul Lone
- Department of Pathology and Microbiology, University of Nebraska Medical Centre, Omaha, Nebraska, United States
| | - Shiva Kumar Yerra
- Department of Cardiology, Mahavir Hospital and Research Centre Hyderabad (Telangana), India
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Sanghera DK, Hopkins R, Malone-Perez MW, Bejar C, Tan C, Mussa H, Whitby P, Fowler B, Rao CV, Fung KA, Lightfoot S, Frazer JK. Targeted sequencing of candidate genes of dyslipidemia in Punjabi Sikhs: Population-specific rare variants in GCKR promote ectopic fat deposition. PLoS One 2019; 14:e0211661. [PMID: 31369557 PMCID: PMC6675050 DOI: 10.1371/journal.pone.0211661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022] Open
Abstract
Dyslipidemia is a well-established risk factor for cardiovascular diseases. Although, advances in genome-wide technologies have enabled the discovery of hundreds of genes associated with blood lipid phenotypes, most of the heritability remains unexplained. Here we performed targeted resequencing of 13 bona fide candidate genes of dyslipidemia to identify the underlying biological functions. We sequenced 940 Sikh subjects with extreme serum levels of hypertriglyceridemia (HTG) and 2,355 subjects were used for replication studies; all 3,295 participants were part of the Asian Indians Diabetic Heart Study. Gene-centric analysis revealed burden of variants for increasing HTG risk in GCKR (p = 2.1x10-5), LPL (p = 1.6x10-3) and MLXIPL (p = 1.6x10-2) genes. Of these, three missense and damaging variants within GCKR were further examined for functional consequences in vivo using a transgenic zebrafish model. All three mutations were South Asian population-specific and were largely absent in other multiethnic populations of Exome Aggregation Consortium. We built different transgenic models of human GCKR with and without mutations and analyzed the effects of dietary changes in vivo. Despite the short-term of feeding, profound phenotypic changes were apparent in hepatocyte histology and fat deposition associated with increased expression of GCKR in response to a high fat diet (HFD). Liver histology of the GCKRmut showed severe fatty metamorphosis which correlated with ~7 fold increase in the mRNA expression in the GCKRmut fish even in the absence of a high fat diet. These findings suggest that functionally disruptive GCKR variants not only increase the risk of HTG but may enhance ectopic lipid/fat storage defects in absence of obesity and HFD. To our knowledge, this is the first transgenic zebrafish model of a putative human disease gene built to accurately assess the influence of genetic changes and their phenotypic consequences in vivo.
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Affiliation(s)
- Dharambir K. Sanghera
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Ruth Hopkins
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Megan W. Malone-Perez
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Cynthia Bejar
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Chengcheng Tan
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Huda Mussa
- Department of Pediatrics, Section of Infectious Diseases, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Paul Whitby
- Department of Pediatrics, Section of Infectious Diseases, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Ben Fowler
- Oklahoma Medical Research Foundation, Imaging Core Facility, Oklahoma City, Oklahoma, United States of America
| | - Chinthapally V. Rao
- Center for Cancer Prevention and Drug Development, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - KarMing A. Fung
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, Oklahoma, United States of America
| | - Stan Lightfoot
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, Oklahoma, United States of America
| | - J. Kimble Frazer
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
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18
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Kim HK, Anwar MA, Choi S. Association of BUD13-ZNF259-APOA5-APOA1-SIK3 cluster polymorphism in 11q23.3 and structure of APOA5 with increased plasma triglyceride levels in a Korean population. Sci Rep 2019; 9:8296. [PMID: 31165758 PMCID: PMC6549162 DOI: 10.1038/s41598-019-44699-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
In this association study on chromosome 11, the data from 12,537 Korean individuals within the Health Examinee (HEXA) and the Korea Association Resource (KARE) projects were analysed to identify genetic loci correlating with increased and decreased plasma triglyceride (TG) levels. We identified a locus in chromosomal region 11q23.3 that harbours genes BUD13, ZNF259, APOA5, APOA1, and SIK3, which may be associated with plasma TG levels. In this locus, 13 relevant single-nucleotide polymorphisms (SNPs) were found: rs184616707, rs118175510, rs60954647, rs79408961, and rs180373 (near BUD13); rs11604424 (in ZNF259); rs2075291, rs651821, and rs7123666 (in or near APOA5); rs525028 (near APOA1), and rs645258, rs10160754, and rs142395187 (in or near SIK3). All 13 SNPs satisfied the genome-wide significance level (P < 5.0 × 10-8) in both meta-analysis and conditional analysis. Haplotype analysis of six SNPs (rs79408961, rs180373, rs2075291, rs651821, rs525028, and rs10160754) that were selected based on the β coefficient and conditional P values, revealed nine common haplotypes (with frequency 0.02-0.34) associated with both increased and reduced TG levels. Furthermore, to shed light on possible structural implications, we modelled and simulated the G185C variant of APOA5 (corresponding to rs2075291), which showed the strongest association. Molecular dynamics simulation results showed that this polymorphic variant of APOA5 has a different hydrogen bond network, increased average distance between chains, and an ability to form distinct clusters. Owing to the orientation of cysteine, the possibility of disulphide bond formation with other proteins is evident. In summary, our association and modelling analyses provided evidence that genetic variations in chromosomal region 11q23.3 are associated with elevated TG levels.
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Affiliation(s)
- Han-Kyul Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Korea
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Korea.
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Impact of gender and age on the association of the BUD13-ZNF259 rs964184 polymorphism with coronary heart disease. Anatol J Cardiol 2019; 19:42-49. [PMID: 29339699 PMCID: PMC5864789 DOI: 10.14744/anatoljcardiol.2017.8002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Coronary heart disease (CHD) is the most common cause of death worldwide. This study aimed to validate the association of the rs964184 polymorphism with the CHD risk and included 874 CHD patients and 776 controls. METHODS rs964184 polymorphism genotyping was performed using Tm-shift polymerase chain reaction. RESULTS A strong association of the rs964184 polymorphism with CHD was found (genotype: X2=14.365, p=0.001; allele: X2=14.191, p=1.67x10-4; power=0.965). Gender analysis revealed a significant association only in males (genotype: X2=12.387, p=0.002; allele: X2=12.404, p=4.32x10-4; OR=1.467, 95% CI=1.185-1.817, power=0.945). Age and gender analyses revealed significant associations of the rs964184 polymorphism with CHD in males between the ages of 55 and 65 years (genotype: X2=10.070, p=0.007; allele: X2=10.077, p=0.002; OR=1.706, 95% CI=1.224-2.377, power=0.996) and in females older than 65 years (genotype: X2=9.462, p=0.009; allele: X2=9.560, p=0.002; OR=2.112, 95% CI=1.308-3.412, power=0.994). Further subgroup analysis suggested that rs964184 genotypes were significantly associated with TG levels in the patients (r=0.191, adjusted p=1.05x10-5) and controls (r=0.101, adjusted p=0.026). CONCLUSION Our results indicate that both gender and age have great impacts on the association of the rs964184 polymorphism with CHD among Chinese.
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Sanghera DK, Bejar C, Sharma S, Gupta R, Blackett PR. Obesity genetics and cardiometabolic health: Potential for risk prediction. Diabetes Obes Metab 2019; 21:1088-1100. [PMID: 30667137 PMCID: PMC6530772 DOI: 10.1111/dom.13641] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 02/06/2023]
Abstract
The increasing burden of obesity worldwide and its effect on cardiovascular disease (CVD) risk is an opportunity for evaluation of preventive approaches. Both obesity and CVD have a genetic background and polymorphisms within genes which enhance expression of variant proteins that influence CVD in obesity. Genome-based prediction may therefore be a feasible strategy, but the identification of genetically driven risk factors for CVD manifesting as clinically recognized phenotypes is a major challenge. Clusters of such risk factors include hyperglycaemia, hypertension, ectopic liver fat, and inflammation. All involve multiple genetic pathways having complex interactions with variable environmental influences. The factors that make significant contributions to CVD risk include altered carbohydrate homeostasis, ectopic deposition of fat in muscle and liver, and inflammation, with contributions from the gut microbiome. A futuristic model depends on harnessing the predictive power of plausible genetic variants, phenotype reversibility, and effective therapeutic choices based on genotype-phenotype interactions. Inverting disease phenotypes into ideal cardiovascular health metrics could improve genetic and epigenetic assessment, and form the basis of a future model for risk detection and early intervention.
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Affiliation(s)
- Dharambir K. Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- (Corresponding authors) Dharambir K. Sanghera, Ph.D., F.A.H.A., Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm. D317 BMSB, Oklahoma City, OK 73104, USA, , Piers R. Blackett, M.D., Department of Pediatrics, Section of Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA,
| | - Cynthia Bejar
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sonali Sharma
- Department of Biochemistry, College of Medical Sciences, Rajasthan University of Health Sciences, Kumbha Marg, Pratap Nagar, Jaipur 302033, India
| | - Rajeev Gupta
- Academic Research Development Unit, College of Medical Sciences, Rajasthan University of Health Sciences, Kumbha Marg, Pratap Nagar, Jaipur 302033, India
| | - Piers R. Blackett
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- (Corresponding authors) Dharambir K. Sanghera, Ph.D., F.A.H.A., Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm. D317 BMSB, Oklahoma City, OK 73104, USA, , Piers R. Blackett, M.D., Department of Pediatrics, Section of Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA,
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21
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Hosseinzadeh N, Mehrabi Y, Daneshpour MS, Zayeri F, Guity K, Azizi F. Identifying new associated pleiotropic SNPs with lipids by simultaneous test of multiple longitudinal traits: An Iranian family-based study. Gene 2019; 692:156-169. [DOI: 10.1016/j.gene.2019.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/05/2019] [Accepted: 01/11/2019] [Indexed: 02/08/2023]
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22
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Bandesh K, Prasad G, Giri AK, Kauser Y, Upadhyay M, Basu A, Tandon N, Bharadwaj D. Genome-wide association study of blood lipids in Indians confirms universality of established variants. J Hum Genet 2019; 64:573-587. [PMID: 30911093 DOI: 10.1038/s10038-019-0591-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/02/2019] [Accepted: 03/03/2019] [Indexed: 12/30/2022]
Abstract
Lipids foster energy production and their altered levels have been coupled with metabolic ailments. Indians feature high prevalence of metabolic diseases, yet uncharacterized for genes regulating lipid homeostasis. We performed first GWAS for quantitative lipids (total cholesterol, LDL, HDL, and triglycerides) exclusively in 5271 Indians. Further to corroborate our genetic findings, we investigated DNA methylation marks in peripheral blood in Indians at the identified loci (N = 233) and retrieved gene regulatory features from public domains. Recurrent GWAS loci-CELSR2, CETP, LPL, ZNF259, and BUD13 cropped up as lead signals in Indians, reflecting their universal applicability. Besides established variants, we found certain unreported variants at sub-genome-wide level-QKI, REEP3, TMCC2, FAM129C, FAM241B, and LOC100506207. These variants though failed to attain GWAS significance in Indians, but largely turned out to be active CpG sites in human subcutaneous adipose tissue and showed robust association to two or more lipid traits. Of which, QKI variants showed significant association to all four lipid traits and their designated region was observed to be a key gene regulatory segment denoting active transcription particularly in human subcutaneous adipose tissue. Both established and novel loci were observed to be significantly associated with altered DNA methylation in Indians for specific CpGs that resided in key regulatory elements. Further, gene-based association analysis pinpointed novel GWAS loci-LINC01340 and IQCJ-SCHIP1 for TC; IFT27, IFT88, and LINC02141 for HDL; and TEX26 for TG. Present study ascertains universality of selected known genes and also identifies certain novel loci for lipids in Indians by integrating data from various levels of gene regulation.
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Affiliation(s)
- Khushdeep Bandesh
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110020, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
| | - Gauri Prasad
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110020, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
| | - Anil K Giri
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110020, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
| | - Yasmeen Kauser
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110020, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
| | - Medha Upadhyay
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | | | - Analabha Basu
- National Institute of Biomedical Genomics, P.O.: Netaji Subhas Sanatorium, Kalyani, 741251, West Bengal, India
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India. .,Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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23
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There is an association between a genetic polymorphism in the ZNF259 gene involved in lipid metabolism and coronary artery disease. Gene 2019; 704:80-85. [PMID: 30902787 DOI: 10.1016/j.gene.2019.02.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/09/2019] [Accepted: 02/22/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent genome-wide association studies (GWAS) have identified several genetic variants that influence the risk of dyslipidemia and coronary artery disease (CAD). In this study, we have examined the potential association of five SNPs variants related to lipid pathway, previously identified in GWAS studies (ZNF259 C>G, CETP I405VA/G, LPA C>T, LPLS447X and PSRC1 A>G) with CAD. METHODS Two hundred and ninety subjects including 194 patients with coronary artery disease and 96 controls were enrolled, followed by the analyses of anthropometric/biochemical parameters. Genotyping was carried out using Taq-Man real-time PCR based method. The association of the genetic polymorphisms with CAD was determined using univariate and multivariate analyses. RESULTS CAD patients had a higher (p < 0.05) fasting blood glucose (FBG), total cholesterol (TC), high sensitivity C-reactive protein (hs-CRP), low-density lipoprotein cholesterol (LDL-C) and waist circumference. Results showed that subjects with CETP rs5882 genetic variant, AA&AG genotypes, had a higher risk of developing Coronary artery disease [OR: 2.1, 95% CI (1.2-4.1), p value = 0.015]. Also subjects who carried the G allele of the ZNF259 polymorphism were at an increased the risk of developing CAD [OR 1.86, 95% CI: 1.06-3.25, p value = 0.029] and had an increased TC, LDL and TG levels (p < 0.05). Furthermore, no statistically significant association was found between genetic polymorphisms of PSRC1 A>G, LPL S447X and LPA C>T and CAD. CONCLUSION We identified a relationship between a genetic variant in CETP and ZNF259 gene with CAD and CAD and lipid profile, respectively. Further investigation in a larger population may help to investigate the value of emerging marker as a risk stratification marker in CAD and its risk factors.
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Bai W, Kou C, Zhang L, You Y, Yu W, Hua W, Li Y, Yu Y, Zhao T, Wu Y. Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern. PeerJ 2019; 6:e6175. [PMID: 30631647 PMCID: PMC6322487 DOI: 10.7717/peerj.6175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/26/2018] [Indexed: 12/14/2022] Open
Abstract
Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy-Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exploration.
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Affiliation(s)
- Wei Bai
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Changgui Kou
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Lili Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Yueyue You
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Weiying Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Wanqing Hua
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Yuanyuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Yaqin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Tiancheng Zhao
- Department of Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China
| | - Yanhua Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China.,Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin Province, China
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Sakamoto K, Bultot L, Göransson O. The Salt-Inducible Kinases: Emerging Metabolic Regulators. Trends Endocrinol Metab 2018; 29:827-840. [PMID: 30385008 DOI: 10.1016/j.tem.2018.09.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 01/08/2023]
Abstract
The discovery of liver kinase B1 (LKB1) as an upstream kinase for AMP-activated protein kinase (AMPK) led to the identification of several related kinases that also rely on LKB1 for their catalytic activity. Among these, the salt-inducible kinases (SIKs) have emerged as key regulators of metabolism. Unlike AMPK, SIKs do not respond to nucleotides, but their function is regulated by extracellular signals, such as hormones, through complex LKB1-independent mechanisms. While AMPK acts on multiple targets, including metabolic enzymes, to maintain cellular ATP levels, SIKs primarily regulate gene expression, by acting on transcriptional regulators, such as the cAMP response element-binding protein-regulated transcription coactivators and class IIa histone deacetylases. This review describes the development of research on SIKs, from their discovery to the most recent findings on metabolic regulation.
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Affiliation(s)
- Kei Sakamoto
- Nestlé Research, EPFL Innovation Park, Bâtiment G, 1015 Lausanne, Switzerland.
| | - Laurent Bultot
- Nestlé Research, EPFL Innovation Park, Bâtiment G, 1015 Lausanne, Switzerland; Current address: Université catholique de Louvain, Institut de Recherche Expérimentale et Clinique, Pole of Cardiovascular Research, Brussels, Belgium
| | - Olga Göransson
- Department of Experimental Medical Science, Lund University, BMC C11, 221 84 Lund, Sweden.
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26
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Moon S, Lee Y, Won S, Lee J. Multiple genotype-phenotype association study reveals intronic variant pair on SIDT2 associated with metabolic syndrome in a Korean population. Hum Genomics 2018; 12:48. [PMID: 30382898 PMCID: PMC6211397 DOI: 10.1186/s40246-018-0180-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
Background Metabolic syndrome is a risk factor for type 2 diabetes and cardiovascular disease. We identified common genetic variants that alter the risk for metabolic syndrome in the Korean population. To isolate these variants, we conducted a multiple-genotype and multiple-phenotype genome-wide association analysis using the family-based quasi-likelihood score (MFQLS) test. For this analysis, we used 7211 and 2838 genotyped study subjects for discovery and replication, respectively. We also performed a multiple-genotype and multiple-phenotype analysis of a gene-based single-nucleotide polymorphism (SNP) set. Results We found an association between metabolic syndrome and an intronic SNP pair, rs7107152 and rs1242229, in SIDT2 gene at 11q23.3. Both SNPs correlate with the expression of SIDT2 and TAGLN, whose products promote insulin secretion and lipid metabolism, respectively. This SNP pair showed statistical significance at the replication stage. Conclusions Our findings provide insight into an underlying mechanism that contributes to metabolic syndrome. Electronic supplementary material The online version of this article (10.1186/s40246-018-0180-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sanghoon Moon
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju, Chungcheongbuk-do, 28159, South Korea
| | - Young Lee
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju, Chungcheongbuk-do, 28159, South Korea.,Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, 05368, South Korea
| | - Sungho Won
- Department of Public Health Science, Seoul National University, Seoul, 08826, South Korea
| | - Juyoung Lee
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju, Chungcheongbuk-do, 28159, South Korea.
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Sanghera DK, Bejar C, Sapkota B, Wander GS, Ralhan S. Frequencies of poor metabolizer alleles of 12 pharmacogenomic actionable genes in Punjabi Sikhs of Indian Origin. Sci Rep 2018; 8:15742. [PMID: 30356105 PMCID: PMC6200732 DOI: 10.1038/s41598-018-33981-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/28/2018] [Indexed: 12/28/2022] Open
Abstract
Diversity in drug response is attributed to both genetic and non-genetic factors. However, there is paucity of pharmacogenetics information across ethnically and genetically diverse populations of India. Here, we have analyzed 21 SNPs from 12 pharmacogenomics genes in Punjabi Sikhs of Indian origin (N = 1,616), as part of the Sikh Diabetes Study (SDS). We compared the allele frequency of poor metabolism (PM) phenotype among Sikhs across other major global populations from the Exome Aggregation Consortium and 1000 Genomes. The PM phenotype of CYP1A2*1 F for slow metabolism of caffeine and carcinogens was significantly higher in Indians (SDS 42%, GIH [Gujarati] 51%, SAS [Pakistani] 45%) compared to Europeans 29% (pgenotype = 5.3E-05). Similarly, South Asians had a significantly higher frequency of CYP2C9*3 (12% SDS, 13% GIH, 11% SAS) vs. 7% in Europeans (pgenotype = <1.0E-05) and ‘T’ allele of CYP4F2 (36%) SDS, (43%) GIH, 40% (SAS) vs. (29%) in Europeans (pgenotype = <1.0E-05); both associated with a higher risk of bleeding with warfarin. All South Asians –the Sikhs (0.36), GIH (0.34), and SAS (0.36) had a higher frequency of the NAT2*6 allele (linked with slow acetylation of isoniazid) compared to Europeans (0.29). Additionally, the prevalence of the low activity ‘C’ allele of MTHFR (rs1801131) was highest in Sikhs compared to all other ethnic groups [SDS (44%), GIH (39%), SAS (42%) and European (32%) (pgenotype = <1.0E-05)]. SNPs in MTHFR affect metabolism of statins, 5-fluorouracil and methotrexate-based cancer drugs. These findings underscore the need for evaluation of other endogamous ethnic groups of India and beyond for establishing a global benchmark for pre-emptive genotyping in drug metabolizing genes before beginning therapeutic intervention.
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Affiliation(s)
- Dharambir K Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Cynthia Bejar
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Bishwa Sapkota
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Sarju Ralhan
- Hero DMC Heart Institute, Ludhiana, Punjab, India
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Hsueh WC, Nair AK, Kobes S, Chen P, Göring HHH, Pollin TI, Malhotra A, Knowler WC, Baier LJ, Hanson RL. Identity-by-Descent Mapping Identifies Major Locus for Serum Triglycerides in Amerindians Largely Explained by an APOC3 Founder Mutation. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001809. [PMID: 29237685 DOI: 10.1161/circgenetics.117.001809] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Identity-by-descent mapping using empirical estimates of identity-by-descent allele sharing may be useful for studies of complex traits in founder populations, where hidden relationships may augment the inherent genetic information that can be used for localization. METHODS AND RESULTS Through identity-by-descent mapping, using ≈400 000 single-nucleotide polymorphisms (SNPs), of serum lipid profiles, we identified a major linkage signal for triglycerides in 1007 Pima Indians (LOD=9.23; P=3.5×10-11 on chromosome 11q). In subsequent fine-mapping and replication association studies in ≈7500 Amerindians, we determined that this signal reflects effects of a loss-of-function Ala43Thr substitution in APOC3 (rs147210663) and 3 established functional SNPs in APOA5. The association with rs147210663 was particularly strong; each copy of the Thr allele conferred 42% lower triglycerides (β=-0.92±0.059 SD unit; P=9.6×10-55 in 4668 Pimas and 2793 Southwest Amerindians combined). The Thr allele is extremely rare in most global populations but has a frequency of 2.5% in Pimas. We further demonstrated that 3 APOA5 SNPs with established functional impact could explain the association with the most well-replicated SNP (rs964184) for triglycerides identified by genome-wide association studies. Collectively, these 4 SNPs account for 6.9% of variation in triglycerides in Pimas (and 4.1% in Southwest Amerindians), and their inclusion in the original linkage model reduced the linkage signal to virtually null. CONCLUSIONS APOC3/APOA5 constitutes a major locus for serum triglycerides in Amerindians, especially the Pimas, and these results provide an empirical example for the concept that population-based linkage analysis is a useful strategy to identify complex trait variants.
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Affiliation(s)
- Wen-Chi Hsueh
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.).
| | - Anup K Nair
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Sayuko Kobes
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Peng Chen
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Harald H H Göring
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Toni I Pollin
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Alka Malhotra
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - William C Knowler
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Leslie J Baier
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Robert L Hanson
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
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Garcia-Rios A, Alcala-Diaz JF, Gomez-Delgado F, Delgado-Lista J, Marin C, Leon-Acuña A, Camargo A, Rodriguez-Cantalejo F, Blanco-Rojo R, Quintana-Navarro G, Ordovas JM, Perez-Jimenez F, Lopez-Miranda J, Perez-Martinez P. Beneficial effect of CETP gene polymorphism in combination with a Mediterranean diet influencing lipid metabolism in metabolic syndrome patients: CORDIOPREV study. Clin Nutr 2018; 37:229-234. [DOI: 10.1016/j.clnu.2016.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 11/09/2016] [Accepted: 12/11/2016] [Indexed: 12/27/2022]
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Aguilar-Salinas CA, Sevilla González MDR, Tusie-Luna MT. Searching for the Causal Variants of the Association Between Hypertriglyceridemia and the Genome-Wide Association Studies-Derived Signals? Take a Look in the Native American Populations. CIRCULATION. CARDIOVASCULAR GENETICS 2017; 10:CIRCGENETICS.117.002010. [PMID: 29237696 DOI: 10.1161/circgenetics.117.002010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Carlos A Aguilar-Salinas
- From the Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, México City, México (C.A.A.-S., M.d.R.S.G.); Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, México (C.A.A.-S., M.d.R.S.G.); Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (M.T.T.-L.); and Instituto Nacional de Ciencias Médicas y Nutrición, México City, México (M.T.T.-L.).
| | - Magdalena Del Rocío Sevilla González
- From the Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, México City, México (C.A.A.-S., M.d.R.S.G.); Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, México (C.A.A.-S., M.d.R.S.G.); Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (M.T.T.-L.); and Instituto Nacional de Ciencias Médicas y Nutrición, México City, México (M.T.T.-L.)
| | - María Teresa Tusie-Luna
- From the Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, México City, México (C.A.A.-S., M.d.R.S.G.); Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, México (C.A.A.-S., M.d.R.S.G.); Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (M.T.T.-L.); and Instituto Nacional de Ciencias Médicas y Nutrición, México City, México (M.T.T.-L.)
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Zhang L, You Y, Wu Y, Zhang Y, Wang M, Song Y, Liu X, Kou C. Association of BUD13 polymorphisms with metabolic syndrome in Chinese population: a case-control study. Lipids Health Dis 2017; 16:127. [PMID: 28659142 PMCID: PMC5490231 DOI: 10.1186/s12944-017-0520-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/16/2017] [Indexed: 11/26/2022] Open
Abstract
Background BUD13 homolog (BUD13), one of submits of the retention and splicing complex, was identified in yeast as a splicing factor that affected nuclear pre-mRNA retention. While more and more studies demonstrated that BUD13 played a potential role in the pathogenesis of metabolic syndrome (MetS). This objective was to reassess whether novel locus of BUD13 were linked to MetS and individual complements in the northeast of China. Methods A total of 3850 individuals were recruited in this case-control study, including 1813 MetS cases and 2037 healthy controls. The diagnostic criteria was according to the International Diabetes Federation (IDF). Metabolic complements such as waist circumference (WC), triglyceride, high-density lipoprotein cholesterol (HDL-C), systolic and diastolic blood pressure (SBP and DBP), and fasting glucose were measured. We explored the association between two novel single nucleotide polymorphism (SNPs) of BUD13 (rs7118999 and rs10488698) and MetS and its complements. Results Using binary logistic regression analysis we found that there were no significant associations between SNPs and MetS in different heritance models (all P > 0.05). However, novel locus of BUD13 were linked to individual complements in MetS cases. Rs7118999 conferred to risk of WC (P = 0.016) and the carrier of TT might have higher susceptibility to MetS. While rs10488698 was associated with HDL-C (P = 0.001) and the carrier of TT was significantly associated with higher level of HDL-C. Conclusions We concluded that novel mutations in BUD13 did not confer risk for MetS in our study population, but these mutations changed the level of metabolic complements.
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Affiliation(s)
- Lili Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Yueyue You
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Yanhua Wu
- Division of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Yangyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Mohan Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Yan Song
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Xinyu Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China
| | - Changgui Kou
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, No. 1163 Xinmin Street, Changchun, Jilin province, 130021, China.
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Pranavchand R, Reddy BM. Quantitative trait loci at the 11q23.3 chromosomal region related to dyslipidemia in the population of Andhra Pradesh, India. Lipids Health Dis 2017; 16:116. [PMID: 28610615 PMCID: PMC5470178 DOI: 10.1186/s12944-017-0507-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 05/31/2017] [Indexed: 02/08/2023] Open
Abstract
Background Given the characteristic atherogenic dyslipidemia of south Indian population and crucial role of APOA1, APOC3, APOA4 and APOA5 genes clustered in 11q23.3 chromosomal region in regulating lipoprotein metabolism and cholesterol homeostasis, a large number of recently identified variants are to be explored for their role in regulating the serum lipid parameters among south Indians. Methods Using fluidigm SNP genotyping platform, a prioritized set of 96 SNPs of the 11q23.3 chromosomal region were genotyped on 516 individuals from Hyderabad, India, and its vicinity and aged >45 years. Results The linear regression analysis of the individual lipid traits viz., TC, LDLC, HDLC, VLDL and TG with each of the 78 SNPs that confirm to HWE and with minor allele frequency > 1%, suggests 23 of those to be significantly associated (p ≤ 0.05) with at least one of these quantitative traits. Most importantly, the variant rs632153 is involved in elevating TC, LDLC, TG and VLDLs and probably playing a crucial role in the manifestation of dyslipidemia. Additionally, another three SNPs rs633389, rs2187126 and rs1263163 are found risk conferring to dyslipidemia by elevating LDLC and TC levels in the present population. Further, the ROC (receiver operating curve) analysis for the risk scores and dyslipidemia status yielded a significant area under curve (AUC) = 0.675, suggesting high discriminative power of the risk variants towards the condition. The interaction analysis suggests rs10488699-rs2187126 pair of the BUD13 gene to confer significant risk (Interaction odds ratio = 14.38, P = 7.17 × 105) towards dyslipidemia by elevating the TC levels (β = 37.13, p = 6.614 × 105). On the other hand, the interaction between variants of APOA1 gene and BUD13 and/or ZPR1 regulatory genes at this region are associated with elevated TG and VLDL. Conclusion The variants at 11q23.3 chromosomal region seem to determine the quantitative lipid traits and in turn dyslipidemia in the population of Hyderabad. Particularly, the variants rs632153, rs633389, rs2187126 and rs1263163 might be risk conferring to dyslipidemia by elevating LDLC and TC levels, while the variants of APOC3 and APOA1 genes might be the genetic determinants of elevated triglycerides in the present population. Electronic supplementary material The online version of this article (doi:10.1186/s12944-017-0507-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rayabarapu Pranavchand
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hyderabad, Telangana, India
| | - Battini Mohan Reddy
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hyderabad, Telangana, India.
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Ayyappa KA, Shatwan I, Bodhini D, Bramwell LR, Ramya K, Sudha V, Anjana RM, Lovegrove JA, Mohan V, Radha V, Vimaleswaran KS. High fat diet modifies the association of lipoprotein lipase gene polymorphism with high density lipoprotein cholesterol in an Asian Indian population. Nutr Metab (Lond) 2017; 14:8. [PMID: 28115978 PMCID: PMC5247808 DOI: 10.1186/s12986-016-0155-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/17/2016] [Indexed: 01/11/2023] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) in lipoprotein lipase gene (LPL) have been shown to influence metabolism related to lipid phenotypes. Dietary factors have been shown to modify the association between LPL SNPs and lipids; however, to date, there are no studies in South Asians. Hence, we tested for the association of four common LPL SNPs with plasma lipids and examined the interactions between the SNPs and dietary factors on lipids in 1,845 Asian Indians. Methods The analysis was performed in 788 Type 2 diabetes cases and 1,057 controls randomly chosen from the cross-sectional Chennai Urban Rural Epidemiological Study. Serum triacylglycerol (TAG), serum total cholesterol, and high-density lipoprotein cholesterol (HDL-C) were measured using a Hitachi-912 autoanalyzer (Roche Diagnostics GmbH, Mannheim, Germany). Dietary intake was assessed using a semi-quantitative food frequency questionnaire. The SNPs (rs1121923, rs328, rs4922115 and rs285) were genotyped by polymerase chain reaction followed by restriction enzyme digestion and 20% of samples were sequenced to validate the genotypes obtained. Statistical Package for Social Sciences for Windows version 22.0 (SPSS, Chicago, IL) was used for statistical analysis. Results After correction for multiple testing and adjusting for potential confounders, SNPs rs328 and rs285 showed association with HDL-C (P = 0.0004) and serum TAG (P = 1×10−5), respectively. The interaction between SNP rs1121923 and fat intake (energy %) on HDL-C (P = 0.003) was also significant, where, among those who consumed a high fat diet (28.4 ± 2.5%), the T allele carriers (TT + XT) had significantly higher HDL-C concentrations (P = 0.0002) and 30% reduced risk of low HDL-C levels compared to the CC homozygotes. None of the interactions on other lipid traits were statistically significant. Conclusion Our findings suggest that individuals carrying T allele of the SNP rs1121923 have increased HDL-C levels when consuming a high fat diet compared to CC homozygotes. Our finding warrants confirmation in prospective studies and randomized controlled trials. Electronic supplementary material The online version of this article (doi:10.1186/s12986-016-0155-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- K A Ayyappa
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Kallam Anji Reddy Centre, Plot no. 20, Golden Jubilee Biotech Park for Women Society, SIPCOT-IT PARK, Siruseri, Chennai 603 103 India.,Present Address: Department of Biotechnology, School of Chemical & Biotechnology, SASTRA University, Tanjore, India
| | - I Shatwan
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP UK.,Food and Nutrition Department, Faculty of Home Economics, King Abdulaziz University, Jeddah, Saudi Arabia
| | - D Bodhini
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Kallam Anji Reddy Centre, Plot no. 20, Golden Jubilee Biotech Park for Women Society, SIPCOT-IT PARK, Siruseri, Chennai 603 103 India
| | - L R Bramwell
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP UK
| | - K Ramya
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Kallam Anji Reddy Centre, Plot no. 20, Golden Jubilee Biotech Park for Women Society, SIPCOT-IT PARK, Siruseri, Chennai 603 103 India
| | - V Sudha
- Department of Foods, Nutrition and Dietetics Research, Madras Diabetes Research Foundation, Chennai, India
| | - R M Anjana
- Department of Diabetology, Madras Diabetes Research Foundation, Chennai, India.,Dr. Mohan's Diabetes Specialties Centre, WHO Collaborating Centre for Non-communicable Diseases Prevention and Control, Chennai, India
| | - J A Lovegrove
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP UK
| | - V Mohan
- Department of Diabetology, Madras Diabetes Research Foundation, Chennai, India.,Dr. Mohan's Diabetes Specialties Centre, WHO Collaborating Centre for Non-communicable Diseases Prevention and Control, Chennai, India
| | - V Radha
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Kallam Anji Reddy Centre, Plot no. 20, Golden Jubilee Biotech Park for Women Society, SIPCOT-IT PARK, Siruseri, Chennai 603 103 India
| | - K S Vimaleswaran
- Department of Food and Nutritional Sciences, Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP UK
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Lin E, Kuo PH, Liu YL, Yang AC, Kao CF, Tsai SJ. Association and interaction of APOA5, BUD13, CETP, LIPA and health-related behavior with metabolic syndrome in a Taiwanese population. Sci Rep 2016; 6:36830. [PMID: 27827461 PMCID: PMC5101796 DOI: 10.1038/srep36830] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/21/2016] [Indexed: 12/17/2022] Open
Abstract
Increased risk of developing metabolic syndrome (MetS) has been associated with the APOA5, APOC1, BRAP, BUD13, CETP, LIPA, LPL, PLCG1, and ZPR1 genes. In this replication study, we reassessed whether these genes are associated with MetS and its individual components independently and/or through complex interactions in a Taiwanese population. We also analyzed the interactions between environmental factors and these genes in influencing MetS and its individual components. A total of 3,000 Taiwanese subjects were assessed in this study. Metabolic traits such as waist circumference, triglyceride, high-density lipoprotein (HDL) cholesterol, systolic and diastolic blood pressure, and fasting glucose were measured. Our data showed a nominal association of MetS with the APOA5 rs662799, BUD13 rs11216129, BUD13 rs623908, CETP rs820299, and LIPA rs1412444 single nucleotide polymorphisms (SNPs). Moreover, APOA5 rs662799, BUD13 rs11216129, and BUD13 rs623908 were significantly associated with high triglyceride, low HDL, triglyceride, and HDL levels. Additionally, we found the interactions of APOA5 rs662799, BUD13 rs11216129, BUD13 rs623908, CETP rs820299, LIPA rs1412444, alcohol consumption, smoking status, or physical activity on MetS and its individual components. Our study indicates that the APOA5, BUD13, CETP, and LIPA genes may contribute to the risk of MetS independently as well as through gene-gene and gene-environment interactions.
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Affiliation(s)
- Eugene Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Vita Genomics, Inc., Taipei, Taiwan.,TickleFish Systems Corporation, Seattle, WA, USA
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
| | - Chung-Feng Kao
- Department of Agronomy, College of Agriculture &Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
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Pranav Chand R, Kumar AS, Anuj K, Vishnupriya S, Mohan Reddy B. Distinct Patterns of Association of Variants at 11q23.3 Chromosomal Region with Coronary Artery Disease and Dyslipidemia in the Population of Andhra Pradesh, India. PLoS One 2016; 11:e0153720. [PMID: 27257688 PMCID: PMC4892567 DOI: 10.1371/journal.pone.0153720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/01/2016] [Indexed: 12/20/2022] Open
Abstract
In our attempt to comprehensively understand the nature of association of variants at 11q23.3 apolipoprotein gene cluster region, we genotyped a prioritized set of 96 informative SNPs using Fluidigm customized SNP genotyping platform in a sample of 508 coronary artery disease (CAD) cases and 516 controls. We found 12 SNPs as significantly associated with CAD at P <0.05, albeit only four (rs2849165, rs17440396, rs6589566 and rs633389) of these remained significant after Benjamin Hochberg correction. Of the four, while rs6589566 confers risk to CAD, the other three SNPs reduce risk for the disease. Interaction of variants that belong to regulatory genes BUD13 and ZPR1 with APOA5-APOA4 intergenic variants is also observed to significantly increase the risk towards CAD. Further, ROC analysis of the risk scores of the 12 significant SNPs suggests that our study has substantial power to confer these genetic variants as predictors of risk for CAD, as illustrated by AUC (0.763; 95% CI: 0.729-0.798, p = <0.0001). On the other hand, the protective SNPs of CAD are associated with elevated Low Density Lipoprotein Cholesterol and Total Cholesterol levels, hence with dyslipidemia, in our sample of controls, which may suggest distinct effects of the variants at 11q23.3 chromosomal region towards CAD and dyslipidemia. It may be necessary to replicate these findings in the independent and ethnically heterogeneous Indian samples in order to establish this as an Indian pattern. However, only functional analysis of the significant variants identified in our study can provide more precise understanding of the mechanisms involved in the contrasting nature of their effects in manifesting dyslipidemia and CAD.
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Affiliation(s)
| | | | - Kapadia Anuj
- Department of Cardiology, Care Hospitals, Hyderabad, India
| | | | - Battini Mohan Reddy
- Molecular Anthropology Group, Indian Statistical Institute, Hyderabad, India
- * E-mail:
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Abstract
Coronary artery disease (CAD) has emerged as a major cause of morbidity and mortality worldwide. Recent findings on the role of genetic factors in the aetiopathology of CAD have implicated novel genes and variants in addition to those involved in lipid and lipoprotein metabolism. However, our present knowledge is limited due to lack of clarity on their exact identity and the quantum of impact on disease susceptibility, and incident risk. It is a matter of great interest to understand the role of genetic factors in ethnic populations that have a strong underlying predisposition to CAD such as the South Asian populations, particularly among Asian Indians living in India and abroad. Although, a number of isolated studies do implicate certain gene polymorphisms towards enhanced disease susceptibility, the available data remains scanty and inconclusive as they have not been validated in large, prospective cohorts. The present review aims to consolidate the available literature on the genetics of CAD in Asian Indians and seeks to provide insights on the concerns that need to be addressed in future studies to generate information having clinical value.
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Wakil SM, Ram R, Muiya NP, Andres E, Mazhar N, Hagos S, Alshahid M, Meyer BF, Morahan G, Dzimiri N. A common variant association study reveals novel susceptibility loci for low HDL-cholesterol levels in ethnic Arabs. Clin Genet 2016; 90:518-525. [PMID: 26879886 DOI: 10.1111/cge.12761] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/08/2016] [Accepted: 02/11/2016] [Indexed: 01/08/2023]
Abstract
The genetic susceptibility to acquiring low high density lipoprotein-cholesterol (LHDLC) levels is not completely elucidated yet. In this study, we performed a common variant association study for harboring this trait in ethnic Arabs. We employed the Affymetrix high-density Axiom Genome-Wide ASI Array (Asian population) providing a coverage of 598,000 single nucleotide variations (SNPs) to genotype 5495 individuals in a two-phase study involving discovery and validation sets of experiments. The rs1800775 [1.31 (1.22-1.42); p = 3.41E-12] in the CETP gene and rs359027 [1.26 (1.16-1.36); p = 2.55E-08] in the LMCD1 gene were significantly associated with LHDLC levels. Furthermore, rs3104435 [1.26 (1.15-1.38); p = 1.19E-06] at the MATN1 locus, rs9835344 [1.16 (1.08-1.26); p = 8.75E-06] in the CNTN6 gene, rs1559997 [1.3 (1.14-1.47); p = 9.48E-06] in the SDS gene and rs1670273 [1.2 (1.1-1.31); p = 4.81E-06] in the DMN/SYNM gene exhibited suggestive association with the disorder. Seven other variants including rs1147169 in the PLCL1 gene, rs10248618 in the DNAH11, rs476155 in the GLIS3, rs7024300 in the ABCA1, intergenic rs10836699, rs11603691 in P2RX3 and rs750134 in CORO1C gene exhibited borderline protective properties. Validation and joint meta-analysis resulted in rs1800775, rs3104435 and rs359027 retaining their predisposing properties, while rs10836699 and rs11603691 showed protective properties. Our data show several predisposing variants across the genome for LHDLC levels in ethnic Arabs.
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Affiliation(s)
- S M Wakil
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - R Ram
- Western Australian Institute for Medical Research, University of Western Australia, Perth, Australia
| | - N P Muiya
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - E Andres
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - N Mazhar
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - S Hagos
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - M Alshahid
- King Faisal Heart Institute, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - B F Meyer
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - G Morahan
- Western Australian Institute for Medical Research, University of Western Australia, Perth, Australia
| | - N Dzimiri
- Genetics Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
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Kurano M, Tsukamoto K, Kamitsuji S, Kamatani N, Hara M, Ishikawa T, Kim BJ, Moon S, Jin Kim Y, Teramoto T. Genome-wide association study of serum lipids confirms previously reported associations as well as new associations of common SNPs within PCSK7 gene with triglyceride. J Hum Genet 2016; 61:427-33. [DOI: 10.1038/jhg.2015.170] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/23/2015] [Accepted: 12/13/2015] [Indexed: 12/31/2022]
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Investigation of associations between ten polymorphisms and the risk of coronary artery disease in Southern Han Chinese. J Hum Genet 2016; 61:389-93. [PMID: 26740236 DOI: 10.1038/jhg.2015.158] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 11/08/2022]
Abstract
A large-scale meta-analysis of 14 genome-wide association studies has identified and replicated a series of susceptibility polymorphisms for coronary artery disease (CAD) in European ancestry populations, but evidences for the associations of these loci with CAD in other ethnicities remain lacking. Herein we investigated the associations between ten (rs579459, rs12413409, rs964184, rs4773144, rs2895811, rs3825807, rs216172, rs12936587, rs46522 and rs3798220) of these loci and CAD in Southern Han Chinese (CHS). Genotyping was performed in 1716 CAD patients and 1572 controls using mass spectrography. Both allelic and genotypic associations of rs964184, rs2895811 and rs3798220 with CAD were significant, regardless of adjustment for covariates of gender, age, hypertension, type 2 diabetes, blood lipid profiles and smoking. Significant association of rs12413409 was initially not observed, but after the adjustment for the covariates, both allelic and genotypic associations were identified as significant. Neither allelic nor genotypic association of the other six polymorphisms with CAD was significant regardless of the adjustment. Our results indicated that four loci of the total 10 were associated with CAD in CHS. Therefore, some of the CAD-related loci in European ancestry populations are indeed susceptibility loci for the risk of CAD in Han Chinese.
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Mirhafez SR, Avan A, Pasdar A, Khatamianfar S, Hosseinzadeh L, Ganjali S, Movahedi A, Pirhoushiaran M, Mellado VG, Rosace D, van Krieken A, Nohtani M, Ferns GA, Ghayour-Mobarhan M. Zinc Finger 259 Gene Polymorphism rs964184 is Associated with Serum Triglyceride Levels and Metabolic Syndrome. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2016; 5:8-18. [PMID: 27386434 PMCID: PMC4916779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Metabolic syndrome (MetS) is characterized by a cluster of cardiovascular risk factors that include: abdominal obesity, dyslipidaemia, hypertension, insulin resistance and impaired glucose tolerance. Recent genome wide association studies have identified several susceptibility regions involved in lipid metabolism that are also associated with MetS. We have explored the association of 9 genetic polymorphisms involved in lipid metabolism and hypertension, including: MTHFR C677T, SELE L554F, FGB - 455G>A, GNB3 C825T, ZNF259 C>G, PSRC-1 A>G, CETP I405V, LPL S447X and LPA C>T in 97 subjects with MetS and 96 individuals without MetS who were recruited randomly from Mashhad stroke and heart atherosclerotic disorder (MASHAD) study using a stratified cluster random sampling technique. Anthropometric parameters and biochemical measurements were determined in all the subjects. Genotyping was carried out followed by univariate and multivariate analyses. The subjects with MetS had a higher triglyceride and lower HDL- C. CG+ GG genotypes of ZNF259 polymorphism (rs964184 C>G) and TT+CT genotypes of MTHFR C677T (rs1801133) were associated with MetS, and individuals carrying the G allele for ZNF259 or the T allele for MTHFR polymorphisms were associated with MetS (e.g, odds ratio (OR) for CG+GG genotypes vs. CC wild type: 2.52, CI=1.33-4.77; P=0.005). However, after multiple comparison adjustment, this relationship remained significant only for CG+ GG genotypes of ZNF259 polymorphism. Moreover, the ZNF259 CG+ GG genotypes were associated with increased serum concentrations of triglycerides and LDL-C, compared to the wild type. These data support the necessity for further studies in larger multicenter settings.
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Affiliation(s)
- Seyed Reza Mirhafez
- Department of Basic Medical Sciences, Neyshabur University of Medical Sciences, Neyshabur, Iran.,Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Alireza Pasdar
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Sara Khatamianfar
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Leila Hosseinzadeh
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Shiva Ganjali
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Ali Movahedi
- Department of Basic Medical Sciences, Neyshabur University of Medical Sciences, Neyshabur, Iran.
| | - Maryam Pirhoushiaran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Valentina Gómez Mellado
- VU University Medical Center, Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | | | - Anne van Krieken
- Peter MacCallum Centre, St Andrew's Place, Melbourne, Australia.
| | - Mahdi Nohtani
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Gordon A. Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK.
| | - Majid Ghayour-Mobarhan
- Department of Modern Science and Technologies; and Biochemistry of Nutrition Research Center; School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Corresponding author: Biochemistry of Nutrition Research Center, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran.
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41
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Zhou S, Zhao J, Wang Z, Li K, Nie S, Gao F, Sun J, Gao X, Huang Y. Association study of BUD13-ZNF259 gene rs964184 polymorphism and hemorrhagic stroke risk. Int J Clin Exp Med 2015; 8:22503-22508. [PMID: 26885234 PMCID: PMC4730020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/03/2015] [Indexed: 06/05/2023]
Abstract
We aimed to evaluate the association of rs964184 of BUD13-ZNF259 gene with the risk of hemorrhagic stroke (HS). A total of 138 HS cases and 587 controls were recruited for the association of rs964184 of BUD13-ZNF259 gene with the risk of HS. Tm shift PCR was used for genotyping. We were unable to find the association of rs964184 of BUD13-ZNF259 gene with the risk of HS (P>0.05). Significant difference was found in the TG level among the three genotypes (CC: 1.51±1.02; CG: 1.68±1.10; GG: 1.90±1.11, P=0.036). The TG level showed strong correlation with rs964184 genotypes (P=0.010, correlation=0.101). Significantly higher TC, HDL-C, and LDL-C levels were observed in the case group. And no difference was found in the TG, ApoA-I, ApoB. Our case-control study supported the significant association between rs964184 genotype and the blood TG concentration, although we were unable to find association between BUD13-ZNF259 rs964184 and the risk of HS in Han Chinese.
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Affiliation(s)
- Shengjun Zhou
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Jikuang Zhao
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Zhepei Wang
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Keqin Li
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Sheng Nie
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Feng Gao
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Jie Sun
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Xiang Gao
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
| | - Yi Huang
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University Ningbo 315010, Zhejiang, China
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Gombojav B, Lee SJ, Kho M, Song YM, Lee K, Sung J. Multiple susceptibility loci at chromosome 11q23.3 are associated with plasma triglyceride in East Asians. J Lipid Res 2015; 57:318-24. [PMID: 26634697 DOI: 10.1194/jlr.p063461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/30/2022] Open
Abstract
Genetic studies of plasma TG levels have identified associations with multiple candidate loci on chromosome11q23.3, which harbors a number of genes, including BUD13, ZNF259, and APOA5-A4-C3-A1. This study aimed to examine whether these multiple candidate genes on the 11q23.3 regions exert independent effects on TG levels or whether their effects are confounded by linkage disequilibrium (LD). We performed a genome-wide association study and consequent fine-mapping analyses on TG levels in two Korean population-based cohorts: the Korea Association Resource study (n = 8,223) and the Healthy Twin study (n = 1,735). A total of 301 loci reached genome-wide significance level in pooled analysis, including 10 SNPs with weak LD (r(2) < 0.06) clustered on 11q23.3: ApoA5 (rs651821, rs2075291); ZNF259 (rs964184, rs603446); BUD13 (rs11216126); Apoa4 (rs7396851); SIK3 (rs12292858); PCSK7 (rs199890178); PAFAH1B2 (rs12420127), and SIDT2 (rs2269399). When the inter-dependence between alleles was examined using conditional models, five loci on BUD13, ZNF259, and ApoA5 showed possible independent associations. A haplotype analysis using five SNPs revealed both hyper- and hypotriglyceridemic haplotypes, which are relatively common in Koreans (haplotype frequency 0.08-0.22). Our findings suggest the presence of multiple functional loci on 11q23.3, which might exert their effects on plasma TG level independently or through complex interactions between functional loci.
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Affiliation(s)
- Bayasgalan Gombojav
- Institute of Health and Environment, Seoul National University, Seoul, Korea Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
| | - Soo Ji Lee
- Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea
| | - Minjung Kho
- Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center and Center for Clinical Research, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kayoung Lee
- Department of Family Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Joohon Sung
- Institute of Health and Environment, Seoul National University, Seoul, Korea Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea
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Fu Q, Tang X, Chen J, Su L, Zhang M, Wang L, Jing J, Zhou L. Effects of Polymorphisms in APOA4-APOA5-ZNF259-BUD13 Gene Cluster on Plasma Levels of Triglycerides and Risk of Coronary Heart Disease in a Chinese Han Population. PLoS One 2015; 10:e0138652. [PMID: 26397108 PMCID: PMC4580433 DOI: 10.1371/journal.pone.0138652] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/02/2015] [Indexed: 01/06/2023] Open
Abstract
Background/Aim Recent genome-wide association studies have identified several loci influencing lipid levels. The present study focused on the triglycerides (TG)-associated locus, the APOA4-APOA5-ZNF259-BUD13 gene cluster on chromosome 11, to explore the role of genetic variants in this gene cluster in the development of increasing TG levels and coronary heart disease (CHD). Methodology/Principal Findings Six single nucleotide polymorphisms (SNPs), rs4417316, rs651821, rs6589566, rs7396835, rs964184 and rs17119975, in the APOA4-APOA5-ZNF259-BUD13 gene cluster were selected and genotyped in 5374 healthy Chinese subjects. There were strong significant associations between the six SNPs and TG levels (P<1.0×10−8). Moreover, a weighted genotype score was found to be associated with TG levels (P = 3.28×10−13). The frequencies of three common haplotypes were observed to be significantly different between the high TG group and the low TG group (P<0.05). However, no significant effects were found for the SNPs regarding susceptibility to CHD in the Chinese case-control populations. Conclusions/Significance This study highlights the genotypes, genotype scores and haplotypes of the APOA4-APOA5-ZNF259-BUD13 gene cluster that were associated with TG levels in a Chinese population; however, the genetic variants in this gene cluster did not increase the risk of CHD in the Chinese population.
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Affiliation(s)
- Qianxi Fu
- Department of Epidemiology, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaojun Tang
- Department of Epidemiology, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
| | - Juan Chen
- The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Li Su
- Department of Cardiology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Mingjun Zhang
- Molecular Medicine and Tumor Research Center, Chongqing Medical University, Yuzhong District in Chongqing, 400016, China
| | - Long Wang
- Department of Epidemiology, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
| | - Jinjin Jing
- The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Li Zhou
- Department of Epidemiology, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- * E-mail:
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Yu W, Kwon MS, Park T. Multivariate Quantitative Multifactor Dimensionality Reduction for Detecting Gene-Gene Interactions. Hum Hered 2015. [PMID: 26201702 DOI: 10.1159/000377723] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To determine gene-gene interactions and missing heritability of complex diseases is a challenging topic in genome-wide association studies. The multifactor dimensionality reduction (MDR) method is one of the most commonly used methods for identifying gene-gene interactions with dichotomous phenotypes. For quantitative phenotypes, the generalized MDR or quantitative MDR (QMDR) methods have been proposed. These methods are known as univariate methods because they consider only one phenotype. To date, there are few methods for analyzing multiple phenotypes. METHODS To address this problem, we propose a multivariate QMDR method (Multi-QMDR) for multivariate correlated phenotypes. We summarize the multivariate phenotypes into a univariate score by dimensional reduction analysis, and then classify the samples accordingly into high-risk and low-risk groups. We use different ways of summarizing mainly based on the principal components. Multi-QMDR is model-free and easy to implement. RESULTS Multi-QMDR is applied to lipid-related traits. The properties of Multi- QMDR were investigated through simulation studies. Empirical studies show that Multi-QMDR outperforms existing univariate and multivariate methods at identifying causal interactions. CONCLUSIONS The Multi-QMDR approach improves the performance of QMDR when multiple quantitative phenotypes are available.
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Affiliation(s)
- Wenbao Yu
- Department of Statistic, Seoul National University, Seoul, South Korea
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45
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Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model. Genetics 2015; 200:59-68. [PMID: 25724382 DOI: 10.1534/genetics.114.171447] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/16/2015] [Indexed: 11/18/2022] Open
Abstract
Multiple-trait association mapping, in which multiple traits are used simultaneously in the identification of genetic variants affecting those traits, has recently attracted interest. One class of approaches for this problem builds on classical variance component methodology, utilizing a multitrait version of a linear mixed model. These approaches both increase power and provide insights into the genetic architecture of multiple traits. In particular, it is possible to estimate the genetic correlation, which is a measure of the portion of the total correlation between traits that is due to additive genetic effects. Unfortunately, the practical utility of these methods is limited since they are computationally intractable for large sample sizes. In this article, we introduce a reformulation of the multiple-trait association mapping approach by defining the matrix-variate linear mixed model. Our approach reduces the computational time necessary to perform maximum-likelihood inference in a multiple-trait model by utilizing a data transformation. By utilizing a well-studied human cohort, we show that our approach provides more than a 10-fold speedup, making multiple-trait association feasible in a large population cohort on the genome-wide scale. We take advantage of the efficiency of our approach to analyze gene expression data. By decomposing gene coexpression into a genetic and environmental component, we show that our method provides fundamental insights into the nature of coexpressed genes. An implementation of this method is available at http://genetics.cs.ucla.edu/mvLMM.
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46
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Sortilin, Encoded by the Cardiovascular Risk Gene SORT1, and Its Suggested Functions in Cardiovascular Disease. Curr Atheroscler Rep 2015; 17:496. [DOI: 10.1007/s11883-015-0496-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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47
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Laston SL, Voruganti VS, Haack K, Shah VO, Bobelu A, Bobelu J, Ghahate D, Harford AM, Paine SS, Tentori F, Cole SA, MacCluer JW, Comuzzie AG, Zager PG. Genetics of kidney disease and related cardiometabolic phenotypes in Zuni Indians: the Zuni Kidney Project. Front Genet 2015; 6:6. [PMID: 25688259 PMCID: PMC4311707 DOI: 10.3389/fgene.2015.00006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
The objective of this study is to identify genetic factors associated with chronic kidney disease (CKD) and related cardiometabolic phenotypes among participants of the Genetics of Kidney Disease in Zuni Indians study. The study was conducted as a community-based participatory research project in the Zuni Indians, a small endogamous tribe in rural New Mexico. We recruited 998 members from 28 extended multigenerational families, ascertained through probands with CKD who had at least one sibling with CKD. We used the Illumina Infinium Human1M-Duo version 3.0 BeadChips to type 1.1 million single nucleotide polymorphisms (SNPs). Prevalence estimates for CKD, hyperuricemia, diabetes, and hypertension were 24%, 30%, 17% and 34%, respectively. We found a significant (p < 1.58 × 10-7) association for a SNP in a novel gene for serum creatinine (PTPLAD2). We replicated significant associations for genes with serum uric acid (SLC2A9), triglyceride levels (APOA1, BUD13, ZNF259), and total cholesterol (PVRL2). We found novel suggestive associations (p < 1.58 × 10-6) for SNPs in genes with systolic (OLFML2B), and diastolic blood pressure (NFIA). We identified a series of genes associated with CKD and related cardiometabolic phenotypes among Zuni Indians, a population with a high prevalence of kidney disease. Illuminating genetic variations that modulate the risk for these disorders may ultimately provide a basis for novel preventive strategies and therapeutic interventions.
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Affiliation(s)
- Sandra L Laston
- South Texas Diabetes and Obesity Institute, Regional Academic Health Center, University of Texas at San Antonio Harlingen, TX, USA
| | - V Saroja Voruganti
- Department of Nutrition, University of North Carolina at Chapel Hill Kannapolis, NC, USA ; University of North Carolina Nutrition Research Institute, University of North Carolina at Chapel Hill Kannapolis, NC, USA
| | - Karin Haack
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA
| | - Vallabh O Shah
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Arlene Bobelu
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Jeanette Bobelu
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Donica Ghahate
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Antonia M Harford
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | | | | | - Shelley A Cole
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA
| | - Jean W MacCluer
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA ; Southwest National Primate Research Center San Antonio, TX, USA
| | - Philip G Zager
- Dialysis Clinic, Inc., Albuquerque, NM USA ; Department of Medicine, Division of Nephrology, University of New Mexico School of Medicine Albuquerque, NM, USA
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48
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Wang XJ, Zhang DL, Xu ZG, Ma ML, Wang WB, Li LL, Han XL, Huo Y, Yu X, Sun JP. Understanding cadherin EGF LAG seven-pass G-type receptors. J Neurochem 2014; 131:699-711. [PMID: 25280249 DOI: 10.1111/jnc.12955] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/05/2014] [Accepted: 09/22/2014] [Indexed: 12/21/2022]
Abstract
The cadherin epidermal growth factor (EGF) laminin G (LAG) seven-pass G-type receptors (CELSRs) are a special subgroup of adhesion G protein-coupled receptors, which are pivotal regulators of many biologic processes such as neuronal/endocrine cell differentiation, vessel valve formation, and the control of planar cell polarity during embryonic development. All three members of the CELSR family (CELSR1-3) have large ecto-domains that form homophilic interactions and encompass more than 2000 amino acids. Mutations in the ecto-domain or other gene locations of CELSRs are associated with neural tube defects and other diseases in humans. Celsr knockout (KO) animals have many developmental defects. Therefore, specific agonists or antagonists of CELSR members may have therapeutic potential. Although significant progress has been made regarding the functions and biochemical properties of CELSRs, our knowledge of these receptors is still lacking, especially considering that they are broadly distributed but have few characterized functions in a limited number of tissues. The dynamic activation and inactivation of CELSRs and the presence of endogenous ligands beyond homophilic interactions remain elusive, as do the regulatory mechanisms and downstream signaling of these receptors. Given this motivation, future studies with more advanced cell biology or biochemical tools, such as conditional KO mice, may provide further insights into the mechanisms underlying CELSR function, laying the foundation for the design of new CELSR-targeted therapeutic reagents. The cadherin EGF LAG seven-pass G-type receptors (CELSRs) are a special subgroup of adhesion G protein-coupled receptors (GPCRs), which have large ecto-domains that form homophilic interactions and encompass more than 2000 amino acids. Recent studies have revealed that CELSRs are pivotal regulators of many biological processes, such as neuronal/endocrine cell differentiation, vessel valve formation and the control of planar cell polarity during embryonic development.
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Affiliation(s)
- Xiao-Jing Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, Shandong, China; Department of Cell Biology, Shandong University School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
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49
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Radovica I, Fridmanis D, Silamikelis I, Nikitina-Zake L, Klovins J. Association between CETP, MLXIPL, and TOMM40 polymorphisms and serum lipid levels in a Latvian population. Meta Gene 2014; 2:565-78. [PMID: 25606439 PMCID: PMC4287865 DOI: 10.1016/j.mgene.2014.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/30/2022] Open
Abstract
Background Abnormal lipid levels are considered one of the most significant risk factors for atherosclerosis and coronary artery disease, two of the main causes of death worldwide. Apart from monogenic cases of hypercholesterolemia, most of the common dyslipidemias are caused by a number of low-impact polymorphisms. It has recently been reported that frequent polymorphisms at a large number of loci are significantly associated with one or more blood lipid parameters in many populations. Identifying these associations in different populations and estimating the possible interactions between genetic models are necessary to explain the underlying genetic architecture of the associated loci and their ultimate impact on lipid-associated traits. Methods We estimated the association between 144 common single-nucleotide polymorphisms (SNPs) from published genome-wide association studies and the levels of total cholesterol, low- and high-density lipoprotein–cholesterol, and triglycerides in 1273 individuals from the Genome Database of the Latvian Population. We analyzed a panel of 144 common SNPs with Illumina GoldenGate Genotyping Assays on the Illumina BeadXpress System. Results Ten SNPs at the CETP locus and two at the MLXIPL locus were associated with reduced high-density lipoprotein–cholesterol levels; one SNP at the TOMM40 locus was associated with increased low-density lipoprotein–cholesterol; and four SNPs at the MLXIPL locus were associated with increased log triglyceride levels. There was also a significant correlation between the number of risk alleles and all the lipid parameters, suggesting that the coexistence of many low-impact SNPs has a greater effect on the dyslipidemia phenotype than the individual effects of found SNPs. Conclusion We conclude that the CETP, MLXIPL, and TOMM40 loci are the strongest genetic factors underlying the variability in lipid traits in our population. Genotyping of 144 common SNPs associated with blood lipids in Latvian population 16 common SNPs are associated with blood lipid levels in Latvian population. The number of risk alleles influences the level of blood lipids.
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Affiliation(s)
- I Radovica
- Latvian Biomedical Research and Study Centre, Latvia, Riga
| | - D Fridmanis
- Latvian Biomedical Research and Study Centre, Latvia, Riga
| | - I Silamikelis
- Latvian Biomedical Research and Study Centre, Latvia, Riga
| | | | - J Klovins
- Latvian Biomedical Research and Study Centre, Latvia, Riga
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50
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Walia GK, Gupta V, Aggarwal A, Asghar M, Dudbridge F, Timpson N, Singh NS, Kumar MR, Kinra S, Prabhakaran D, Reddy KS, Chandak GR, Smith GD, Ebrahim S. Association of common genetic variants with lipid traits in the Indian population. PLoS One 2014; 9:e101688. [PMID: 24991929 PMCID: PMC4081649 DOI: 10.1371/journal.pone.0101688] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 06/10/2014] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies (GWAS) have been instrumental in identifying novel genetic variants associated with altered plasma lipid levels. However, these quantitative trait loci have not been tested in the Indian population, where there is a poorly understood and growing burden of cardiometabolic disorders. We present the association of six single nucleotide polymorphisms in 1671 sib pairs (3342 subjects) with four lipid traits: total cholesterol, triglycerides, high density lipoprotein cholesterol (HDL-C) and low density lipoprotein cholesterol (LDL-C). We also investigated the interaction effects of gender, location, fat intake and physical activity. Each copy of the risk allele of rs964184 at APOA1 was associated with 1.06 mmol/l increase in triglycerides (SE = 0.049; p = 0.006), rs3764261 at CETP with 1.02 mmol/l increase in both total cholesterol (SE = 0.042; p = 0.017) and HDL-C (SE = 0.041; p = 0.008), rs646776 at CELSR2-PSRC1-SORT1 with 0.96 mmol/l decrease in cholesterol (SE = 0.043; p = 0.0003) and 0.15 mmol/l decrease in LDL-C levels (SE = 0.043; p = 0.0003) and rs2954029 at TRIB1 with 1.02 mmol/l increase in HDL-C (SE = 0.039; p = 0.047). A combined risk score of APOA1 and CETP loci predicted an increase of 1.25 mmol/l in HDL-C level (SE = 0.312; p = 0.0007). Urban location and sex had strong interaction effects on the genetic association of most of the studied loci with lipid traits. To conclude, we validated four genetic variants (identified by GWAS in western populations) associated with lipid traits in the Indian population. The interaction effects found here may explain the sex-specific differences in lipid levels and their heritability. Urbanization appears to influence the nature of the association with GWAS lipid loci in this population. However, these findings will require replication in other Indian populations.
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Affiliation(s)
- Gagandeep Kaur Walia
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
- * E-mail: (GKW); (VG)
| | - Vipin Gupta
- Department of Anthropology, University of Delhi, Delhi, India
- * E-mail: (GKW); (VG)
| | - Aastha Aggarwal
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
| | - Mohammad Asghar
- Department of Anthropology, Rajiv Gandhi University, Itanagar, Arunachal Pradesh, India
| | - Frank Dudbridge
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nicholas Timpson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | | | - M. Ravi Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Sanjay Kinra
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dorairaj Prabhakaran
- Centre for Chronic Disease Control, New Delhi, India
- Public Health Foundation of India, New Delhi, India
| | | | | | - George Davey Smith
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Shah Ebrahim
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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