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Barupal DK, Ramos ML, Florio AA, Wheeler WA, Weinstein SJ, Albanes D, Fiehn O, Graubard BI, Petrick JL, McGlynn KA. Identification of pre-diagnostic lipid sets associated with liver cancer risk using untargeted lipidomics and chemical set analysis: A nested case-control study within the ATBC cohort. Int J Cancer 2024; 154:454-464. [PMID: 37694774 PMCID: PMC10845132 DOI: 10.1002/ijc.34726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/12/2023]
Abstract
In pre-disposed individuals, a reprogramming of the hepatic lipid metabolism may support liver cancer initiation. We conducted a high-resolution mass spectrometry based untargeted lipidomics analysis of pre-diagnostic serum samples from a nested case-control study (219 liver cancer cases and 219 controls) within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. Out of 462 annotated lipids, 158 (34.2%) were associated with liver cancer risk in a conditional logistic regression analysis at a false discovery rate (FDR) <0.05. A chemical set enrichment analysis (ChemRICH) and co-regulatory set analysis suggested that 22/28 lipid classes and 47/83 correlation modules were significantly associated with liver cancer risk (FDR <0.05). Strong positive associations were observed for monounsaturated fatty acids (MUFA), triacylglycerols (TAGs) and phosphatidylcholines (PCs) having MUFA acyl chains. Negative associations were observed for sphingolipids (ceramides and sphingomyelins), lysophosphatidylcholines, cholesterol esters and polyunsaturated fatty acids (PUFA) containing TAGs and PCs. Stearoyl-CoA desaturase enzyme 1 (SCD1), a rate limiting enzyme in fatty acid metabolism and ceramidases seems to be critical in this reprogramming. In conclusion, our study reports pre-diagnostic lipid changes that provide novel insights into hepatic lipid metabolism reprogramming may contribute to a pro-cell growth and anti-apoptotic tissue environment and, in turn, support liver cancer initiation.
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Affiliation(s)
- Dinesh K Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mark L Ramos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Andrea A Florio
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, California, USA
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jessica L Petrick
- Slone Epidemiology Center at Boston University, Boston, Massachusetts, USA
| | - Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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2
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Brial F, Hedjazi L, Sonomura K, Al Hageh C, Zalloua P, Matsuda F, Gauguier D. Genetic Architecture of Untargeted Lipidomics in Cardiometabolic-Disease Patients Combines Strong Polygenic Control and Pleiotropy. Metabolites 2022; 12:metabo12070596. [PMID: 35888720 PMCID: PMC9322850 DOI: 10.3390/metabo12070596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023] Open
Abstract
Analysis of the genetic control of small metabolites provides powerful information on the regulation of the endpoints of genome expression. We carried out untargeted liquid chromatography−high-resolution mass spectrometry in 273 individuals characterized for pathophysiological elements of the cardiometabolic syndrome. We quantified 3013 serum lipidomic features, which we used in both genome-wide association studies (GWAS), using a panel of over 2.5 M imputed single-nucleotide polymorphisms (SNPs), and metabolome-wide association studies (MWAS) with phenotypes. Genetic analyses showed that 926 SNPs at 551 genetic loci significantly (q-value < 10−8) regulate the abundance of 74 lipidomic features in the group, with evidence of monogenic control for only 22 of these. In addition to this strong polygenic control of serum lipids, our results underscore instances of pleiotropy, when a single genetic locus controls the abundance of several distinct lipid features. Using the LIPID MAPS database, we assigned putative lipids, predominantly fatty acyls and sterol lipids, to 77% of the lipidome signals mapped to the genome. We identified significant correlations between lipids and clinical and biochemical phenotypes. These results demonstrate the power of untargeted lipidomic profiling for high-density quantitative molecular phenotyping in human-genetic studies and illustrate the complex genetic control of lipid metabolism.
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Affiliation(s)
- Francois Brial
- Center for Genomic Medicine, Graduate School of Medicine Kyoto University, Kyoto 606-8501, Japan; (F.B.); (F.M.)
- INSERM UMR 1124, Université Paris Cité, 45 rue des Saint-Pères, 75006 Paris, France
| | | | - Kazuhiro Sonomura
- Life Science Research Center, Technology Research Laboratory, Shimadzu Corporation, Kyoto 606-8501, Japan;
| | - Cynthia Al Hageh
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 17666, United Arab Emirates; (C.A.H.); (P.Z.)
| | - Pierre Zalloua
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 17666, United Arab Emirates; (C.A.H.); (P.Z.)
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine Kyoto University, Kyoto 606-8501, Japan; (F.B.); (F.M.)
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada
| | - Dominique Gauguier
- Center for Genomic Medicine, Graduate School of Medicine Kyoto University, Kyoto 606-8501, Japan; (F.B.); (F.M.)
- INSERM UMR 1124, Université Paris Cité, 45 rue des Saint-Pères, 75006 Paris, France
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada
- Correspondence:
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3
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A multi-omics study of circulating phospholipid markers of blood pressure. Sci Rep 2022; 12:574. [PMID: 35022422 PMCID: PMC8755711 DOI: 10.1038/s41598-021-04446-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/13/2021] [Indexed: 01/02/2023] Open
Abstract
High-throughput techniques allow us to measure a wide-range of phospholipids which can provide insight into the mechanisms of hypertension. We aimed to conduct an in-depth multi-omics study of various phospholipids with systolic blood pressure (SBP) and diastolic blood pressure (DBP). The associations of blood pressure and 151 plasma phospholipids measured by electrospray ionization tandem mass spectrometry were performed by linear regression in five European cohorts (n = 2786 in discovery and n = 1185 in replication). We further explored the blood pressure-related phospholipids in Erasmus Rucphen Family (ERF) study by associating them with multiple cardiometabolic traits (linear regression) and predicting incident hypertension (Cox regression). Mendelian Randomization (MR) and phenome-wide association study (Phewas) were also explored to further investigate these association results. We identified six phosphatidylethanolamines (PE 38:3, PE 38:4, PE 38:6, PE 40:4, PE 40:5 and PE 40:6) and two phosphatidylcholines (PC 32:1 and PC 40:5) which together predicted incident hypertension with an area under the ROC curve (AUC) of 0.61. The identified eight phospholipids are strongly associated with triglycerides, obesity related traits (e.g. waist, waist-hip ratio, total fat percentage, body mass index, lipid-lowering medication, and leptin), diabetes related traits (e.g. glucose, insulin resistance and insulin) and prevalent type 2 diabetes. The genetic determinants of these phospholipids also associated with many lipoproteins, heart rate, pulse rate and blood cell counts. No significant association was identified by bi-directional MR approach. We identified eight blood pressure-related circulating phospholipids that have a predictive value for incident hypertension. Our cross-omics analyses show that phospholipid metabolites in the circulation may yield insight into blood pressure regulation and raise a number of testable hypothesis for future research.
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4
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Yoshinaga MY, Quintanilha BJ, Chaves-Filho AB, Miyamoto S, Sampaio GR, Rogero MM. Postprandial plasma lipidome responses to a high-fat meal among healthy women. J Nutr Biochem 2021; 97:108809. [PMID: 34192591 DOI: 10.1016/j.jnutbio.2021.108809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/27/2021] [Accepted: 06/08/2021] [Indexed: 11/20/2022]
Abstract
Postprandial lipemia consists of changes in concentrations and composition of plasma lipids after food intake, commonly presented as increased levels of triglyceride-rich lipoproteins. Postprandial hypertriglyceridemia may also affect high-density lipoprotein (HDL) structure and function, resulting in a net decrease in HDL concentrations. Elevated triglycerides (TG) and reduced HDL levels have been positively associated with risk of cardiovascular diseases development. Here, we investigated the plasma lipidome composition of 12 clinically healthy, nonobese and young women in response to an acute high-caloric (1135 kcal) and high-fat (64 g) breakfast meal. For this purpose, we employed a detailed untargeted mass spectrometry-based lipidomic approach and data was obtained at four sampling points: fasting and 1, 3 and 5 h postprandial. Analysis of variance revealed 73 significantly altered lipid species between all sampling points. Nonetheless, two divergent subgroups have emerged at 5 h postprandial as a function of differential plasma lipidome responses, and were thereby designated slow and fast TG metabolizers. Late responses by slow TG metabolizers were associated with increased concentrations of several species of TG and phosphatidylinositol (PI). Lipidomic analysis of lipoprotein fractions at 5 h postprandial revealed higher TG and PI concentrations in HDL from slow relative to fast TG metabolizers, but not in apoB-containing fraction. These data indicate that modulations in HDL lipidome during prolonged postprandial lipemia may potentially impact HDL functions. A comprehensive characterization of plasma lipidome responses to acute metabolic challenges may contribute to a better understanding of diet/lifestyle regulation in the metabolism of lipid and glucose.
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Affiliation(s)
- Marcos Yukio Yoshinaga
- Laboratory of Modified Lipids, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
| | - Bruna Jardim Quintanilha
- Nutritional Genomics and Inflammation Laboratory, Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil; Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo, Brazil
| | - Adriano Britto Chaves-Filho
- Laboratory of Modified Lipids, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Laboratory of Modified Lipids, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Geni Rodrigues Sampaio
- Nutritional Genomics and Inflammation Laboratory, Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Marcelo Macedo Rogero
- Nutritional Genomics and Inflammation Laboratory, Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil; Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo, Brazil.
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5
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von Eckardstein A. High Density Lipoproteins: Is There a Comeback as a Therapeutic Target? Handb Exp Pharmacol 2021; 270:157-200. [PMID: 34463854 DOI: 10.1007/164_2021_536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Low plasma levels of High Density Lipoprotein (HDL) cholesterol (HDL-C) are associated with increased risks of atherosclerotic cardiovascular disease (ASCVD). In cell culture and animal models, HDL particles exert multiple potentially anti-atherogenic effects. However, drugs increasing HDL-C have failed to prevent cardiovascular endpoints. Mendelian Randomization studies neither found any genetic causality for the associations of HDL-C levels with differences in cardiovascular risk. Therefore, the causal role and, hence, utility as a therapeutic target of HDL has been questioned. However, the biomarker "HDL-C" as well as the interpretation of previous data has several important limitations: First, the inverse relationship of HDL-C with risk of ASCVD is neither linear nor continuous. Hence, neither the-higher-the-better strategies of previous drug developments nor previous linear cause-effect relationships assuming Mendelian randomization approaches appear appropriate. Second, most of the drugs previously tested do not target HDL metabolism specifically so that the futile trials question the clinical utility of the investigated drugs rather than the causal role of HDL in ASCVD. Third, the cholesterol of HDL measured as HDL-C neither exerts nor reports any HDL function. Comprehensive knowledge of structure-function-disease relationships of HDL particles and associated molecules will be a pre-requisite, to test them for their physiological and pathogenic relevance and exploit them for the diagnostic and therapeutic management of individuals at HDL-associated risk of ASCVD but also other diseases, for example diabetes, chronic kidney disease, infections, autoimmune and neurodegenerative diseases.
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Affiliation(s)
- Arnold von Eckardstein
- Institute of Clinical Chemistry, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
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6
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Qin M, Zhu Q, Lai W, Ma Q, Liu C, Chen X, Zhang Y, Wang Z, Chen H, Yan H, Lei H, Zhang S, Dong X, Wang H, Huang M, Lian Q, Zhong S. Insights into the prognosis of lipidomic dysregulation for death risk in patients with coronary artery disease. Clin Transl Med 2020; 10:e189. [PMID: 32997403 PMCID: PMC7522592 DOI: 10.1002/ctm2.189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Dyslipidaemia contributes to the progression of coronary artery disease (CAD) toward adverse outcomes. Plasma lipidomic measure may improve the prognostic performances of clinical endpoints of CAD. Our research is designed to identify the correlations between plasma lipid species and the risks of death, major adverse cardiovascular event (MACE) and left ventricular (LV) remodeling in patients with CAD. METHODS A total of 1569 Chinese patients with CAD, 1011 single-centre patients as internal training cohort, and 558 multicentre patients as external validation cohort, were enrolled. The concentration of plasma lipids in both cohorts was determined through widely targeted lipidomic profiling. Least absolute shrinkage and selection operator Cox and multivariate Cox regressions were used to develop prognostic models for death and MACE, respectively. RESULTS Ten (Cer(d18:1/20:1), Cer(d18:1/24:1), PE(30:2), PE(32:0), PE(32:2), PC(O-38:2), PC(O-36:4), PC(16:1/22:2), LPC(18:2/0:0) and LPE(0:0/24:6)) and two (Cer(d18:1/20:1) and LPC(20:0/0:0)) lipid species were independently related to death and MACE, respectively. Cer(d18:1/20:1) and Cer(d18:1/24:1) were correlated with LV remodeling (P < .05). The lipidic panel incorporating 10 lipid species and two traditional biomarkers for predicting 5-year death risk represented a remarkable higher discrimination than traditional model with increased area under the curve from 76.56 to 83.65%, continuous NRI of 0.634 and IDI of 0.131. Furthermore, the panel was successfully used in differentiating multicentre patients with low, middle, or high risks (P < .0001). Further analysis indicated that the number of double bonds of phosphatidyl choline and the content of carbon atoms of phosphatidyl ethanolamines were negatively associated with death risk. CONCLUSIONS Improvement in the prediction of death confirms the effectiveness of plasma lipids as predictors to risk classification in patients with CAD. The association between the structural characteristics of long-chain polyunsaturated fatty acids and death risk highlights the need for mechanistic research that characterizes the role of individual lipid species in disease pathogenesis.
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Affiliation(s)
- Min Qin
- Department of PharmacyGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
- School of MedicineSouth China University of TechnologyGuangzhouGuangdongP. R. China
| | - Qian Zhu
- Department of PharmacyGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
- School of MedicineSouth China University of TechnologyGuangzhouGuangdongP. R. China
| | - Weihua Lai
- Department of PharmacyGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
| | - Qilin Ma
- Department of Clinical PharmacologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Chen Liu
- Department of CardiologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdongP. R. China
| | - Xiaoping Chen
- Department of Clinical PharmacologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Yuelin Zhang
- Department of Emergency MedicineDepartment of Emergency and Critical Care MedicineGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
| | - Zixian Wang
- Department of PharmacyGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
- School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouGuangdongP. R. China
| | - Hui Chen
- Department of PharmacyGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
- School of MedicineSouth China University of TechnologyGuangzhouGuangdongP. R. China
| | - Hong Yan
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
- School of MedicineSouth China University of TechnologyGuangzhouGuangdongP. R. China
| | - Heping Lei
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
| | - Shuyao Zhang
- Guangzhou Red Cross Hospital affiliated to Ji‐Nan University Medical CollegeGuangzhouGuangdongP. R. China
| | - Xuekui Dong
- Wuhan Metware Biotechnology Co., Ltd.WuhanHubeiP. R. China
| | - Hong Wang
- Wuhan Metware Biotechnology Co., Ltd.WuhanHubeiP. R. China
| | - Min Huang
- School of Pharmaceutical SciencesInstitute of Clinical PharmacologySun Yat‐Sen UniversityGuangzhouGuangdongP. R. China
| | - Qizhou Lian
- Department of MedicineThe University of Hong KongPokfulamHong Kong
| | - Shilong Zhong
- Department of PharmacyGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease PreventionGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangdong Cardiovascular InstituteGuangzhouGuangdongP. R. China
- School of MedicineSouth China University of TechnologyGuangzhouGuangdongP. R. China
- School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouGuangdongP. R. China
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7
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Liu X, Shi L, Dai X, Chen H, Zhang C, Wang P, Wu Q, Zeng L, Yan H. Plasma metabolites mediate the association of coarse grain intake with blood pressure in hypertension-free adults. Nutr Metab Cardiovasc Dis 2020; 30:1512-1519. [PMID: 32624346 DOI: 10.1016/j.numecd.2020.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Increased intake of whole/coarse grains was associated with improved blood pressure control, but concurrent metabolism alterations are less clear. We sought to identify metabolomic profiles of blood pressure, and to explore their mediation effects on the coarse grain intake-blood pressure association among young adults free of hypertension. METHODS AND RESULTS Plasma metabolome of 86 participants from the Carbohydrate Alternatives and Metabolic Phenotypes study was characterized by untargeted lipidomics and metabolomics using liquid chromatography-high-resolution mass spectrometry. We identified 24 and 117 metabolites associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP), respectively, using random forest modeling and partial correlation analysis. Moreover, metabolite panels for highly specific prediction of blood pressure (8 metabolites for SBP and 11 metabolites for DBP) were determined using ten-fold cross-validated ridge regression (R2 ≥ 0.70). We also observed an inverse association between metabolite panel of SBP (β ± SE = -0.02 ± 0.01, P = 0.04) or DBP (β ± SE = -0.03 ± 0.01, P = 0.02) and coarse grain intake. Furthermore, we observed significant mediating effects of metabolites, in particular, sphingolipid ceramides, on the association between coarse grain exposure and blood pressure using both bias-corrected bootstrap tests and high-dimensional mediation analysis adapted for large-scale and high-throughput omics data. CONCLUSIONS We identified metabolomic profiles specifically associated with blood pressure in young Chinese adults without diagnosed hypertension. The inverse association between coarse grain intake and blood pressure may be mediated by sphingolipid metabolites.
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Affiliation(s)
- Xin Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China.
| | - Lin Shi
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden; School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi' an, 710062, China
| | - Xiaoshuang Dai
- BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, 518083, PR China.
| | - Huangtao Chen
- Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China
| | - Chenglin Zhang
- Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China
| | - Pei Wang
- Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China
| | - Qian Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China
| | - Lingxia Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China
| | - Hong Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China; Nutrition and Food Safety Engineering Research Center of Shaanxi Province, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, 76 West Yanta Road, 710061, Xi'an, Shaanxi, China
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8
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Ekholm J, Ohukainen P, Kangas AJ, Kettunen J, Wang Q, Karsikas M, Khan AA, Kingwell BA, Kähönen M, Lehtimäki T, Raitakari OT, Järvelin MR, Meikle PJ, Ala-Korpela M. EpiMetal: an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics. Int J Epidemiol 2020; 49:1075-1081. [PMID: 31943015 PMCID: PMC7660139 DOI: 10.1093/ije/dyz244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/11/2019] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION An intuitive graphical interface that allows statistical analyses and visualizations of extensive data without any knowledge of dedicated statistical software or programming. IMPLEMENTATION EpiMetal is a single-page web application written in JavaScript, to be used via a modern desktop web browser. GENERAL FEATURES Standard epidemiological analyses and self-organizing maps for data-driven metabolic profiling are included. Multiple extensive datasets with an arbitrary number of continuous and category variables can be integrated with the software. Any snapshot of the analyses can be saved and shared with others via a www-link. We demonstrate the usage of EpiMetal using pilot data with over 500 quantitative molecular measures for each sample as well as in two large-scale epidemiological cohorts (N >10 000). AVAILABILITY The software usage exemplar and the pilot data are open access online at [http://EpiMetal.computationalmedicine.fi]. MIT licensed source code is available at the Github repository at [https://github.com/amergin/epimetal].
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Affiliation(s)
- Jussi Ekholm
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Pauli Ohukainen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | | | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- THL: National Institute for Health and Welfare, Helsinki, Finland
| | - Qin Wang
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mari Karsikas
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Solita Ltd, Tampere, Finland
| | - Anmar A Khan
- Metabolomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Bronwyn A Kingwell
- Metabolic and Vascular Physiology, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Marjo-Riitta Järvelin
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Peter J Meikle
- Metabolomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Alfred Hospital, Monash University, Melbourne, VIC, Australia
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9
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Cadby G, Melton PE, McCarthy NS, Giles C, Mellett NA, Huynh K, Hung J, Beilby J, Dubé MP, Watts GF, Blangero J, Meikle PJ, Moses EK. Heritability of 596 lipid species and genetic correlation with cardiovascular traits in the Busselton Family Heart Study. J Lipid Res 2020; 61:537-545. [PMID: 32060071 DOI: 10.1194/jlr.ra119000594] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/12/2020] [Indexed: 12/22/2022] Open
Abstract
CVD is the leading cause of death worldwide, and genetic investigations into the human lipidome may provide insight into CVD risk. The aim of this study was to estimate the heritability of circulating lipid species and their genetic correlation with CVD traits. Targeted lipidomic profiling was performed on 4,492 participants from the Busselton Family Heart Study to quantify the major fatty acids of 596 lipid species from 33 classes. We estimated narrow-sense heritabilities of lipid species/classes and their genetic correlations with eight CVD traits: BMI, HDL-C, LDL-C, triglycerides, total cholesterol, waist-hip ratio, systolic blood pressure, and diastolic blood pressure. We report heritabilities and genetic correlations of new lipid species/subclasses, including acylcarnitine (AC), ubiquinone, sulfatide, and oxidized cholesteryl esters. Over 99% of lipid species were significantly heritable (h2: 0.06-0.50) and all lipid classes were significantly heritable (h2: 0.14-0.50). The monohexosylceramide and AC classes had the highest median heritabilities (h2 = 0.43). The largest genetic correlation was between clinical triglycerides and total diacylglycerol (rg = 0.88). We observed novel positive genetic correlations between clinical triglycerides and phosphatidylglycerol species (rg: 0.64-0.82), and HDL-C and alkenylphosphatidylcholine species (rg: 0.45-0.74). Overall, 51% of the 4,768 lipid species-CVD trait genetic correlations were statistically significant after correction for multiple comparisons. This is the largest lipidomic study to address the heritability of lipids and their genetic correlation with CVD traits. Future work includes identifying putative causal genetic variants for lipid species and CVD using genome-wide SNP and whole-genome sequencing data.
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Affiliation(s)
- Gemma Cadby
- School of Population and Global Health, University of Western Australia, Crawley, Australia .,Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Phillip E Melton
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Crawley, Australia.,Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia.,School of Biomedical Sciences, Curtin University, Bentley, Australia
| | - Nina S McCarthy
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Corey Giles
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Natalie A Mellett
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Kevin Huynh
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Joseph Hung
- School of Medicine, University of Western Australia, Crawley, Australia.,Department of Cardiovascular Medicine, Nedlands, Australia
| | - John Beilby
- Busselton Population Medical Research Institute Inc., Sir Charles Gairdner Hospital, Busselton, Australia.,PathWest Laboratory Medicine WA, Perth, Australia
| | - Marie-Pierre Dubé
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Montreal, Canada
| | - Gerald F Watts
- School of Medicine, University of Western Australia, Crawley, Australia.,Lipid Disorders Clinic, Department of Cardiology, Royal Perth Hospital, Perth, Australia
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Peter J Meikle
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Crawley, Australia.,Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
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10
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Long NP, Nghi TD, Kang YP, Anh NH, Kim HM, Park SK, Kwon SW. Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine. Metabolites 2020; 10:E51. [PMID: 32013105 PMCID: PMC7074059 DOI: 10.3390/metabo10020051] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.
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Affiliation(s)
- Nguyen Phuoc Long
- College of Pharmacy, Seoul National University, Seoul 08826, Korea; (N.P.L.); (N.H.A.); (H.M.K.)
| | - Tran Diem Nghi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea; (T.D.N.); (S.K.P.)
| | - Yun Pyo Kang
- Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
| | - Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul 08826, Korea; (N.P.L.); (N.H.A.); (H.M.K.)
| | - Hyung Min Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Korea; (N.P.L.); (N.H.A.); (H.M.K.)
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea; (T.D.N.); (S.K.P.)
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul 08826, Korea; (N.P.L.); (N.H.A.); (H.M.K.)
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11
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Sung HH, Sinclair AJ, Huynh K, Smith AT, Mellett NA, Meikle PJ, Su XQ. Differential plasma postprandial lipidomic responses to krill oil and fish oil supplementations in women: A randomized crossover study. Nutrition 2019; 65:191-201. [DOI: 10.1016/j.nut.2019.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/14/2019] [Accepted: 03/01/2019] [Indexed: 10/26/2022]
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12
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Drazba MA, Holásková I, Sahyoun NR, Ventura Marra M. Associations of Adiposity and Diet Quality with Serum Ceramides in Middle-Aged Adults with Cardiovascular Risk Factors. J Clin Med 2019; 8:E527. [PMID: 30999626 PMCID: PMC6517875 DOI: 10.3390/jcm8040527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
Rates of adverse cardiovascular events have increased among middle-aged adults. Elevated ceramides have been proposed as a risk factor for cardiovascular events. Diet quality and weight status are inversely associated with several traditional risk factors; however, the relationship to ceramides is less clear. This study aimed to determine associations of adiposity and diet quality with circulating ceramides in middle-aged adults (n = 96). Diet quality was estimated using the Healthy Eating Index 2015 (HEI-2015). Serum ceramide concentrations were determined by liquid chromatography-mass spectrometry. A ceramide risk score was determined based on ceramides C16:0, C18:0, and C24:1 and their ratios to C24:0. Participants who were classified as at 'moderate risk' compared to 'lower-risk' based on a ceramide risk score had significantly higher body mass index (BMI) values, as well as higher rates of elevated fibrinogen levels, metabolic syndrome, and former smoking status. BMI was positively associated with the ceramide C18:0 (R2 = 0.31, p < 0.0001), the ratio between C18:0/C24:0 ceramides (R2 = 0.30, p < 0.0001), and the ceramide risk score (R2 = 0.11, p < 0.009). Total HEI-2015 scores (R2 = 0.42, p = 0.02), higher intakes of vegetables (R2 = 0.44, p = 0.02) and whole grains (R2 = 0.43, p = 0.03), and lower intakes of saturated fats (R2 = 0.43, p = 0.04) and added sugar (R2 = 0.44, p = 0.01) were associated with lower C22:0 values. These findings suggest that circulating ceramides are more strongly related to adiposity than overall diet quality. Studies are needed to determine if improvements in weight status result in lower ceramides and ceramide risk scores.
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Affiliation(s)
- Margaret A Drazba
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
| | - Ida Holásková
- Office of Statistics, West Virginia University, Davis College of Agriculture, Natural Resources and Design, West Virginia Agriculture and Forestry Experiment Station, Morgantown, WV 26506-6108, USA.
| | - Nadine R Sahyoun
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
| | - Melissa Ventura Marra
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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13
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van der Laan SW, Harshfield EL, Hemerich D, Stacey D, Wood AM, Asselbergs FW. From lipid locus to drug target through human genomics. Cardiovasc Res 2018; 114:1258-1270. [PMID: 29800275 DOI: 10.1093/cvr/cvy120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/16/2018] [Indexed: 12/14/2022] Open
Abstract
In the last decade, over 175 genetic loci have robustly been associated to levels of major circulating blood lipids. Most loci are specific to one or two lipids, whereas some (SUGP1, ZPR1, TRIB1, HERPUD1, and FADS1) are associated to all. While exposing the polygenic architecture of circulating lipids and the underpinnings of dyslipidaemia, these genome-wide association studies (GWAS) have provided further evidence of the critical role that lipids play in coronary heart disease (CHD) risk, as indicated by the 2.7-fold enrichment for macrophage gene expression in atherosclerotic plaques and the association of 25 loci (such as PCSK9, APOB, ABCG5-G8, KCNK5, LPL, HMGCR, NPC1L1, CETP, TRIB1, ABO, PMAIP1-MC4R, and LDLR) with CHD. These GWAS also confirmed known and commonly used therapeutic targets, including HMGCR (statins), PCSK9 (antibodies), and NPC1L1 (ezetimibe). As we head into the post-GWAS era, we offer suggestions for how to move forward beyond genetic risk loci, towards refining the biology behind the associations and identifying causal genes and therapeutic targets. Deep phenotyping through lipidomics and metabolomics will refine and increase the resolution to find causal and druggable targets, and studies aimed at demonstrating gene transcriptional and regulatory effects of lipid associated loci will further aid in identifying these targets. Thus, we argue the need for deeply phenotyped, large genetic association studies to reduce costs and failures and increase the efficiency of the drug discovery pipeline. We conjecture that in the next decade a paradigm shift will tip the balance towards a data-driven approach to therapeutic target development and the application of precision medicine where human genomics takes centre stage.
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Affiliation(s)
- Sander W van der Laan
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Eric L Harshfield
- Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge CB1 8RN, UK
- Department of Clinical Neurosciences, University of Cambridge, R3, Box 83, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Daiane Hemerich
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - David Stacey
- Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge CB1 8RN, UK
| | - Angela M Wood
- Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge CB1 8RN, UK
| | - Folkert W Asselbergs
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
- Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, the Netherlands
- Faculty of Population Health Sciences, Institute of Cardiovascular Science, University College London, London, UK
- Farr Institute of Health Informatics Research, Institute of Health Informatics, University College London, London, UK
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14
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Ala-Korpela M. Objective Metabolomics Research. Clin Chem 2018; 64:30-33. [DOI: 10.1373/clinchem.2017.274852] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/19/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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15
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Würtz P, Kangas AJ, Soininen P, Lawlor DA, Davey Smith G, Ala-Korpela M. Quantitative Serum Nuclear Magnetic Resonance Metabolomics in Large-Scale Epidemiology: A Primer on -Omic Technologies. Am J Epidemiol 2017; 186:1084-1096. [PMID: 29106475 PMCID: PMC5860146 DOI: 10.1093/aje/kwx016] [Citation(s) in RCA: 315] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 01/19/2017] [Indexed: 12/13/2022] Open
Abstract
Detailed metabolic profiling in large-scale epidemiologic studies has uncovered novel biomarkers for cardiometabolic diseases and clarified the molecular associations of established risk factors. A quantitative metabolomics platform based on nuclear magnetic resonance spectroscopy has found widespread use, already profiling over 400,000 blood samples. Over 200 metabolic measures are quantified per sample; in addition to many biomarkers routinely used in epidemiology, the method simultaneously provides fine-grained lipoprotein subclass profiling and quantification of circulating fatty acids, amino acids, gluconeogenesis-related metabolites, and many other molecules from multiple metabolic pathways. Here we focus on applications of magnetic resonance metabolomics for quantifying circulating biomarkers in large-scale epidemiology. We highlight the molecular characterization of risk factors, use of Mendelian randomization, and the key issues of study design and analyses of metabolic profiling for epidemiology. We also detail how integration of metabolic profiling data with genetics can enhance drug development. We discuss why quantitative metabolic profiling is becoming widespread in epidemiology and biobanking. Although large-scale applications of metabolic profiling are still novel, it seems likely that comprehensive biomarker data will contribute to etiologic understanding of various diseases and abilities to predict disease risks, with the potential to translate into multiple clinical settings.
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Affiliation(s)
- Peter Würtz
- Correspondence to Dr. Peter Würtz, Computational Medicine, Faculty of Medicine, Aapistie 5A, P.O. Box 5000, FI-90014 University of Oulu, Finland (e-mail: ); or Dr. Mika Ala-Korpela, Computational Medicine, Faculty of Medicine, Aapistie 5A, P.O. Box 5000, FI-90014 University of Oulu, Finland (e-mail: )
| | | | | | | | | | - Mika Ala-Korpela
- Correspondence to Dr. Peter Würtz, Computational Medicine, Faculty of Medicine, Aapistie 5A, P.O. Box 5000, FI-90014 University of Oulu, Finland (e-mail: ); or Dr. Mika Ala-Korpela, Computational Medicine, Faculty of Medicine, Aapistie 5A, P.O. Box 5000, FI-90014 University of Oulu, Finland (e-mail: )
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16
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Toledo E, Wang DD, Ruiz-Canela M, Clish CB, Razquin C, Zheng Y, Guasch-Ferré M, Hruby A, Corella D, Gómez-Gracia E, Fiol M, Estruch R, Ros E, Lapetra J, Fito M, Aros F, Serra-Majem L, Liang L, Salas-Salvadó J, Hu FB, Martínez-González MA. Plasma lipidomic profiles and cardiovascular events in a randomized intervention trial with the Mediterranean diet. Am J Clin Nutr 2017; 106:973-983. [PMID: 28814398 PMCID: PMC5611779 DOI: 10.3945/ajcn.116.151159] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/19/2017] [Indexed: 12/21/2022] Open
Abstract
Background: Lipid metabolites may partially explain the inverse association between the Mediterranean diet (MedDiet) and cardiovascular disease (CVD).Objective: We evaluated the associations between 1) lipid species and the risk of CVD (myocardial infarction, stroke, or cardiovascular death); 2) a MedDiet intervention [supplemented with extra virgin olive oil (EVOO) or nuts] and 1-y changes in these molecules; and 3) 1-y changes in lipid species and subsequent CVD.Design: With the use of a case-cohort design, we profiled 202 lipid species at baseline and after 1 y of intervention in the PREDIMED (PREvención con DIeta MEDiterránea) trial in 983 participants [230 cases and a random subcohort of 790 participants (37 overlapping cases)].Results: Baseline concentrations of cholesterol esters (CEs) were inversely associated with CVD. A shorter chain length and higher saturation of some lipids were directly associated with CVD. After adjusting for multiple testing, direct associations remained significant for 20 lipids, and inverse associations remained significant for 6 lipids. When lipid species were weighted by the number of carbon atoms and double bonds, the strongest inverse association was found for CEs [HR: 0.39 (95% CI: 0.22, 0.68)] between extreme quintiles (P-trend = 0.002). Participants in the MedDiet + EVOO and MedDiet + nut groups experienced significant (P < 0.05) 1-y changes in 20 and 17 lipids, respectively, compared with the control group. Of these changes, only those in CE(20:3) in the MedDiet + nuts group remained significant after correcting for multiple testing. None of the 1-y changes was significantly associated with CVD risk after correcting for multiple comparisons.Conclusions: Although the MedDiet interventions induced some significant 1-y changes in the lipidome, they were not significantly associated with subsequent CVD risk. Lipid metabolites with a longer acyl chain and higher number of double bonds at baseline were significantly and inversely associated with the risk of CVD.
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Affiliation(s)
- Estefanía Toledo
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
| | | | - Miguel Ruiz-Canela
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
| | | | - Cristina Razquin
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
| | | | | | - Adela Hruby
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University and Tufts University Friedman School of Nutrition Science and Policy, Boston, MA
| | - Dolores Corella
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | | | - Miquel Fiol
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Institute of Health Sciences, University of Balearic Islands and Hospital Son Espases, Palma de Mallorca, Spain
| | - Ramón Estruch
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Departments of Internal Medicine and
| | - Emilio Ros
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Endocrinology and Nutrition, August Pi i Sunyer Biomedical Research Institute Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - José Lapetra
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Department of Family Medicine, Primary Care Division of Sevilla, San Pablo Health Center, Sevilla, Spain
| | - Montserrat Fito
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Cardiovascular and Nutrition Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Fernando Aros
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Department of Cardiology, University Hospital of Alava, Vitoria, Spain
| | - Luis Serra-Majem
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Research Institute of Biomedical and Health Sciences, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Liming Liang
- Epidemiology, and
- Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Jordi Salas-Salvadó
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Human Nutrition Unit, Pere Virgili Institute for Health Research, Rovira i Virgili University, Reus, Spain; and
| | - Frank B Hu
- Departments of Nutrition
- Epidemiology, and
- Department of Medicine, Channing Division for Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Miguel A Martínez-González
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain;
- Navarra Institute for Health Research, Pamplona, Spain
- Biomedical Research Center in Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
- Departments of Nutrition
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17
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Holmes MV, Ala-Korpela M, Smith GD. Mendelian randomization in cardiometabolic disease: challenges in evaluating causality. Nat Rev Cardiol 2017; 14:577-590. [PMID: 28569269 DOI: 10.1038/nrcardio.2017.78] [Citation(s) in RCA: 413] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mendelian randomization (MR) is a burgeoning field that involves the use of genetic variants to assess causal relationships between exposures and outcomes. MR studies can be straightforward; for example, genetic variants within or near the encoding locus that is associated with protein concentrations can help to assess their causal role in disease. However, a more complex relationship between the genetic variants and an exposure can make findings from MR more difficult to interpret. In this Review, we describe some of these challenges in interpreting MR analyses, including those from studies using genetic variants to assess causality of multiple traits (such as branched-chain amino acids and risk of diabetes mellitus); studies describing pleiotropic variants (for example, C-reactive protein and its contribution to coronary heart disease); and those investigating variants that disrupt normal function of an exposure (for example, HDL cholesterol or IL-6 and coronary heart disease). Furthermore, MR studies on variants that encode enzymes responsible for the metabolism of an exposure (such as alcohol) are discussed, in addition to those assessing the effects of variants on time-dependent exposures (extracellular superoxide dismutase), cumulative exposures (LDL cholesterol), and overlapping exposures (triglycerides and non-HDL cholesterol). We elaborate on the molecular features of each relationship, and provide explanations for the likely causal associations. In doing so, we hope to contribute towards more reliable evaluations of MR findings.
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Affiliation(s)
- Michael V Holmes
- Medical Research Council Population Health Research Unit, University of Oxford, Roosevelt Drive, Oxford OX3 7LF, UK.,Clinical Trial Service Unit &Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Big Data Institute Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University Hospital, Old Road, Oxford OX3 7LE, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Mika Ala-Korpela
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, University of Oulu, Aapistie 5A, 90014, Oulu, Finland.,School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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18
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Ala-Korpela M, Davey Smith G. Metabolic profiling-multitude of technologies with great research potential, but (when) will translation emerge? Int J Epidemiol 2016; 45:1311-1318. [PMID: 27789667 PMCID: PMC5100630 DOI: 10.1093/ije/dyw305] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland .,Medical Research Council Integrative Epidemiology Unit and School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit and School of Social and Community Medicine, University of Bristol, Bristol, UK
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19
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Ebrahim S. Metabolomics, nutrition and why epidemiology matters. Int J Epidemiol 2016; 45:1307-1310. [DOI: 10.1093/ije/dyw304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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