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Zhang A, Pan C, Wu M, Lin Y, Chen J, Zhong N, Zhang R, Pu L, Han L, Pan H. Causal association between plasma metabolites and neurodegenerative diseases. Prog Neuropsychopharmacol Biol Psychiatry 2024; 134:111067. [PMID: 38908505 DOI: 10.1016/j.pnpbp.2024.111067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/06/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Establishing causal relationships between metabolic biomarkers and neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD) is a challenge faced by observational studies. In this study, our aim was to investigate the causal associations between plasma metabolites and neurodegenerative diseases using Mendelian Randomization (MR) methods. METHODS We utilized genetic associations with 1400 plasma metabolic traits as exposures. We used large-scale genome-wide association study (GWAS) summary statistics for AD and PD as our discovery datasets. For validation, we performed repeated analyses using different GWAS datasets. The main statistical method employed was inverse variance-weighted (IVW). We also conducted enrichment pathway analysis for IVW-identified metabolites. RESULTS In the discovered dataset, there are a total of 69 metabolites (36 negatively, 33 positively) potentially associated with AD, and 47 metabolites (24 negatively, 23 positively) potentially associated with PD. Among these, 4 significant metabolites overlap with significant metabolites (PIVW < 0.05)in the validation dataset for AD, and 1 metabolite overlaps with significant metabolites in the validation dataset for PD. Three metabolites serve as common potential metabolic markers for both AD and PD, including Tryptophan betaine, Palmitoleoylcarnitine (C16:1), and X-23655 levels. Further pathway enrichment analysis suggests that the SLC-mediated transmembrane transport pathway, involving tryptophan betaine and carnitine metabolites, may represent potential intervention targets for treating AD and PD. CONCLUSION This study offers novel insights into the causal effects of plasma metabolites on degenerative diseases through the integration of genomics and metabolomics. The identification of metabolites and metabolic pathways linked to AD and PD enhances our comprehension of the underlying biological mechanisms and presents promising targets for future therapeutic interventions in AD and PD.
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Affiliation(s)
- Ao Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical University, Dongguan City, Guangdong Province, China
| | - Congcong Pan
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical University, Dongguan City, Guangdong Province, China
| | - Meifen Wu
- Department of Endocrinology, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan City, Guangdong Province, China
| | - Yue Lin
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical University, Dongguan City, Guangdong Province, China
| | - Jiashen Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical University, Dongguan City, Guangdong Province, China
| | - Ni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical University, Dongguan City, Guangdong Province, China
| | - Ruijie Zhang
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life Sciences and Health Industry Research Institute, Chinese Academy of Sciences, Ningbo, Zhejiang Province, China
| | - Liyuan Pu
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life Sciences and Health Industry Research Institute, Chinese Academy of Sciences, Ningbo, Zhejiang Province, China
| | - Liyuan Han
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life Sciences and Health Industry Research Institute, Chinese Academy of Sciences, Ningbo, Zhejiang Province, China.
| | - Haiyan Pan
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Medical University, Dongguan City, Guangdong Province, China.
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2
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Weinisch P, Raffler J, Römisch-Margl W, Arnold M, Mohney RP, Rist MJ, Prehn C, Skurk T, Hauner H, Daniel H, Suhre K, Kastenmüller G. The HuMet Repository: Watching human metabolism at work. Cell Rep 2024; 43:114416. [PMID: 39033506 DOI: 10.1016/j.celrep.2024.114416] [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: 11/09/2023] [Revised: 05/11/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024] Open
Abstract
Metabolism oscillates between catabolic and anabolic states depending on food intake, exercise, or stresses that change a multitude of metabolic pathways simultaneously. We present the HuMet Repository for exploring dynamic metabolic responses to oral glucose/lipid loads, mixed meals, 36-h fasting, exercise, and cold stress in healthy subjects. Metabolomics data from blood, urine, and breath of 15 young, healthy men at up to 56 time points are integrated and embedded within an interactive web application, enabling researchers with and without computational expertise to search, visualize, analyze, and contextualize the dynamic metabolite profiles of 2,656 metabolites acquired on multiple platforms. With examples, we demonstrate the utility of the resource for research into the dynamics of human metabolism, highlighting differences and similarities in systemic metabolic responses across challenges and the complementarity of metabolomics platforms. The repository, providing a reference for healthy metabolite changes to six standardized physiological challenges, is freely accessible through a web portal.
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Affiliation(s)
- Patrick Weinisch
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Raffler
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Digital Medicine, University Hospital of Augsburg, Augsburg, Germany
| | - Werner Römisch-Margl
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | | | - Manuela J Rist
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Cornelia Prehn
- Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Skurk
- ZIEL Institute for Food and Health, Core Facility Human Studies, Technical University of Munich, Freising, Germany; Else Kröner Fresenius Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hans Hauner
- Else Kröner Fresenius Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute for Nutritional Medicine, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Hannelore Daniel
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karsten Suhre
- Department of Biophysics and Physiology, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
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3
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Rahman ML, Shu XO, Jones DP, Hu W, Ji BT, Blechter B, Wong JYY, Cai Q, Yang G, Gao YT, Zheng W, Rothman N, Walker D, Lan Q. A nested case-control study of untargeted plasma metabolomics and lung cancer among never-smoking women within the prospective Shanghai Women's Health Study. Int J Cancer 2024; 155:508-518. [PMID: 38651675 PMCID: PMC11284831 DOI: 10.1002/ijc.34929] [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: 07/27/2023] [Revised: 01/27/2024] [Accepted: 02/12/2024] [Indexed: 04/25/2024]
Abstract
The etiology of lung cancer in never-smokers remains elusive, despite 15% of lung cancer cases in men and 53% in women worldwide being unrelated to smoking. Here, we aimed to enhance our understanding of lung cancer pathogenesis among never-smokers using untargeted metabolomics. This nested case-control study included 395 never-smoking women who developed lung cancer and 395 matched never-smoking cancer-free women from the prospective Shanghai Women's Health Study with 15,353 metabolic features quantified in pre-diagnostic plasma using liquid chromatography high-resolution mass spectrometry. Recognizing that metabolites often correlate and seldom act independently in biological processes, we utilized a weighted correlation network analysis to agnostically construct 28 network modules of correlated metabolites. Using conditional logistic regression models, we assessed the associations for both metabolic network modules and individual metabolic features with lung cancer, accounting for multiple testing using a false discovery rate (FDR) < 0.20. We identified a network module of 121 features inversely associated with all lung cancer (p = .001, FDR = 0.028) and lung adenocarcinoma (p = .002, FDR = 0.056), where lyso-glycerophospholipids played a key role driving these associations. Another module of 440 features was inversely associated with lung adenocarcinoma (p = .014, FDR = 0.196). Individual metabolites within these network modules were enriched in biological pathways linked to oxidative stress, and energy metabolism. These pathways have been implicated in previous metabolomics studies involving populations exposed to known lung cancer risk factors such as traffic-related air pollution and polycyclic aromatic hydrocarbons. Our results suggest that untargeted plasma metabolomics could provide novel insights into the etiology and risk factors of lung cancer among never-smokers.
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Affiliation(s)
- Mohammad L Rahman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Qiuyin Cai
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Gong Yang
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Douglas Walker
- Division of Environmental Health, School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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4
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Lin W, Ji J, Su KJ, Qiu C, Tian Q, Zhao LJ, Luo Z, Wu C, Shen H, Deng H. omicsMIC: a comprehensive benchmarking platform for robust comparison of imputation methods in mass spectrometry-based omics data. NAR Genom Bioinform 2024; 6:lqae071. [PMID: 38881578 PMCID: PMC11177553 DOI: 10.1093/nargab/lqae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/25/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Mass spectrometry is a powerful and widely used tool for generating proteomics, lipidomics and metabolomics profiles, which is pivotal for elucidating biological processes and identifying biomarkers. However, missing values in mass spectrometry-based omics data may pose a critical challenge for the comprehensive identification of biomarkers and elucidation of the biological processes underlying human complex disorders. To alleviate this issue, various imputation methods for mass spectrometry-based omics data have been developed. However, a comprehensive comparison of these imputation methods is still lacking, and researchers are frequently confronted with a multitude of options without a clear rationale for method selection. To address this pressing need, we developed omicsMIC (mass spectrometry-based omics with Missing values Imputation methods Comparison platform), an interactive platform that provides researchers with a versatile framework to evaluate the performance of 28 diverse imputation methods. omicsMIC offers a nuanced perspective, acknowledging the inherent heterogeneity in biological data and the unique attributes of each dataset. Our platform empowers researchers to make data-driven decisions in imputation method selection based on real-time visualizations of the outcomes associated with different imputation strategies. The comprehensive benchmarking and versatility of omicsMIC make it a valuable tool for the scientific community engaged in mass spectrometry-based omics research. omicsMIC is freely available at https://github.com/WQLin8/omicsMIC.
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Affiliation(s)
- Weiqiang Lin
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Jiadong Ji
- Institute for Financial Studies, Shandong University, Jinan, Shandong 250100, China
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chuan Qiu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Lan-Juan Zhao
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhe Luo
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hongwen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
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5
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Li B, Zhao X, Xie W, Hong Z, Cao Y, Ding Y, Zhang Y. Causal association of circulating metabolites with diabetic retinopathy: a bidirectional Mendelian randomization analysis. Front Endocrinol (Lausanne) 2024; 15:1359502. [PMID: 38800471 PMCID: PMC11116606 DOI: 10.3389/fendo.2024.1359502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction The retina is a highly metabolically active tissue, and there is a lack of clarity about the relationship between metabolites and diabetic retinopathy (DR). This study used two-sample bidirectional Mendelian randomization (MR) analyses to identify causal relationships between metabolites and DR. Methods Genetic variants were selected from the open-access Genome-Wide Association Studies (GWAS) summary database as proxies for the 1400 most recently published metabolites. MR analysis was performed to examine associations between these metabolite traits and DR. Single nucleotide polymorphism (SNP) data that were significantly associated with exposure were screened through association analysis. Validated instrumental variables (IVs) were obtained by removing SNPs with linkage disequilibrium (LD) and F-statistic values below 10. MR analyses were performed using the inverse variance weighted (IVW) method as the primary approach. The robustness of the results was verified by sensitivity analyses, including assessments of heterogeneity, horizontal pleiotropy, and the leave-one-out method. Results In the IVW approach and in the primary analysis of several sensitivity analyses, genetically determined glycolithocholate sulfate levels, androstenediol (3 beta, 17 beta) monosulfate (1) levels, 1-stearoyl-2-arachidonoyl-GPE (18:0/20:4) levels, 1-oleoyl-2-arachidonoyl-GPE (18:1/20:4) levels, 1-oleoyl-2-linoleoyl-GPE (18:1/18:2) levels, X-26109 levels, N6-methyllysine levels, (N6,N6-dimethyllysine levels), and (N2-acetyl,N6,N6-dimethyllysine levels) were negatively associated with the risk of DR. 5-hydroxymethyl-2-furoylcarnitine levels and the glutamate-to-alanine ratio were positively associated with the risk of DR. No reverse causal association was found between DR and metabolites. Discussion This MR study suggests that nine metabolites may have a protective effect in DR, while two metabolites may be associated with an increased risk of DR. However, further research is needed to confirm these findings. Supplementation with beneficial metabolites may reduce DR risk and could potentially be a novel therapeutic approach to DR treatment.
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Affiliation(s)
- Bo Li
- Department of Endocrinology, Quanzhou First Hospital, Affiliated to Fujian Medical University, Quanzhou, Fujian, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Biomedical Research Institute, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xu Zhao
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Wanrun Xie
- Department of Endocrinology, Quanzhou First Hospital, Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Zhenzhen Hong
- Department of Endocrinology, Quanzhou First Hospital, Affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Ye Cao
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
- Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yan Ding
- Hubei Key Laboratory of Embryonic Stem Cell Research, Biomedical Research Institute, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yi Zhang
- Department of Endocrinology, Quanzhou First Hospital, Affiliated to Fujian Medical University, Quanzhou, Fujian, China
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6
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Li B, Chen J, Ou X, Liu X, Xu Z, Xiang X, Yang Y, Wang Q. In-depth multiomic characterization of the effects of obesity in high-fat diet-fed mice. FEBS Open Bio 2024; 14:771-792. [PMID: 38479983 PMCID: PMC11073502 DOI: 10.1002/2211-5463.13788] [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: 09/28/2023] [Revised: 12/08/2023] [Accepted: 03/01/2024] [Indexed: 05/07/2024] Open
Abstract
High-fat diet (HFD)-fed mice have been widely used in the clinical investigation of obesity. However, the long-term effect of HFD on gut microbiota and metabolites, plasma and liver metabolomics, colonic and liver transcriptomics remain largely unknown. In this study, 6-week-old C57BL/6J male mice fed with HFD for 14 weeks showed increased obesity-related indexes including alanine aminotransferase, aspartate aminotransferase, total cholesterol, total triglyceride, free fatty acids, lipopolysaccharides, IL-6, and TNFα. Furthermore, microbial diversity and richness were also significantly decreased. In the colon, genes involved in tryptophan metabolism, PPAR signaling pathway, cholesterol metabolism, and lipid localization and transport, were upregulated. While in the liver, MAPK signaling and unsaturated fatty acid biosynthesis were upregulated. Metabolomic analyses revealed decreased levels of glycerophospholipids and fatty acyl, but increased amino acids, coenzymes and vitamins, and organic acids in the colon, suggesting high absorption of oxidized lipids, while acyl-carnitine, lysophosphatidylcholine, lysophosphatidylethanolamine, and oxidized lipids were reduced in the liver, suggesting a more active lipid metabolism. Finally, correlation analyses revealed a positive correlation between gut microbiota and metabolites and the expression of genes associated with lipid localization, absorption, and transport in the colon, and nutrients and energy metabolism in the liver. Taken together, our results provide a comprehensive characterization of long-term HFD-induced obesity in mice.
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Affiliation(s)
- Boping Li
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Medicine, Longdong University, Qingyang, China
| | - Juanjuan Chen
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Xiaobin Ou
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Xiuli Liu
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Zaoxu Xu
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong, Longdong University, Qingyang, China
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Xuesong Xiang
- Element Nutrition of National Health Commission, National Institute of Nutrition and Health, China CDC, Beijing, China
| | - Yan Yang
- Department of Endocrinology and Metabolism, Lanzhou University Second Hospital, Lanzhou, China
| | - Qi Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
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7
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Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW, Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J. Genome-wide characterization of circulating metabolic biomarkers. Nature 2024; 628:130-138. [PMID: 38448586 PMCID: PMC10990933 DOI: 10.1038/s41586-024-07148-y] [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: 11/07/2022] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Genome-wide association analyses using high-throughput metabolomics platforms have led to novel insights into the biology of human metabolism1-7. This detailed knowledge of the genetic determinants of systemic metabolism has been pivotal for uncovering how genetic pathways influence biological mechanisms and complex diseases8-11. Here we present a genome-wide association study for 233 circulating metabolic traits quantified by nuclear magnetic resonance spectroscopy in up to 136,016 participants from 33 cohorts. We identify more than 400 independent loci and assign probable causal genes at two-thirds of these using manual curation of plausible biological candidates. We highlight the importance of sample and participant characteristics that can have significant effects on genetic associations. We use detailed metabolic profiling of lipoprotein- and lipid-associated variants to better characterize how known lipid loci and novel loci affect lipoprotein metabolism at a granular level. We demonstrate the translational utility of comprehensively phenotyped molecular data, characterizing the metabolic associations of intrahepatic cholestasis of pregnancy. Finally, we observe substantial genetic pleiotropy for multiple metabolic pathways and illustrate the importance of careful instrument selection in Mendelian randomization analysis, revealing a putative causal relationship between acetone and hypertension. Our publicly available results provide a foundational resource for the community to examine the role of metabolism across diverse diseases.
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Affiliation(s)
- Minna K Karjalainen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland.
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland.
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Public Health Specialty Training Programme, Cambridge, UK
| | - Eeva Sliz
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elias Allara
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Wing Tung Fung
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kati Kristiansson
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matt Goodwin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matt J Neville
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ayse Demirkan
- Surrey Institute for People-Centred AI, University of Surrey, Guildford, UK
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christiana Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Pashupati P Mishra
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Erin Macdonald-Dunlop
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Jonas Zierer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yara T E Lechanteur
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ivana Kolcic
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Genomics Research Center, Abbvie, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, 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
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tonu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fredrik Karpe
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Perola
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Mika Ala-Korpela
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Johannes Kettunen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
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8
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Qiu H, Zhang X, Zhang Y, Jiang X, Ren Y, Gao D, Zhu X, Usadel B, Fernie AR, Wen W. Depicting the genetic and metabolic panorama of chemical diversity in the tea plant. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1001-1016. [PMID: 38048231 PMCID: PMC10955498 DOI: 10.1111/pbi.14241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023]
Abstract
As a frequently consumed beverage worldwide, tea is rich in naturally important bioactive metabolites. Combining genetic, metabolomic and biochemical methodologies, here, we present a comprehensive study to dissect the chemical diversity in tea plant. A total of 2837 metabolites were identified at high-resolution with 1098 of them being structurally annotated and 63 of them were structurally identified. Metabolite-based genome-wide association mapping identified 6199 and 7823 metabolic quantitative trait loci (mQTL) for 971 and 1254 compounds in young leaves (YL) and the third leaves (TL), respectively. The major mQTL (i.e., P < 1.05 × 10-5, and phenotypic variation explained (PVE) > 25%) were further interrogated. Through extensive annotation of the tea metabolome as well as network-based analysis, this study broadens the understanding of tea metabolism and lays a solid foundation for revealing the natural variations in the chemical composition of the tea plant. Interestingly, we found that galloylations, rather than hydroxylations or glycosylations, were the largest class of conversions within the tea metabolome. The prevalence of galloylations in tea is unusual, as hydroxylations and glycosylations are typically the most prominent conversions of plant specialized metabolism. The biosynthetic pathway of flavonoids, which are one of the most featured metabolites in tea plant, was further refined with the identified metabolites. And we demonstrated the further mining and interpretation of our GWAS results by verifying two identified mQTL (including functional candidate genes CsUGTa, CsUGTb, and CsCCoAOMT) and completing the flavonoid biosynthetic pathway of the tea plant.
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Affiliation(s)
- Haiji Qiu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Xiaoliang Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Youjun Zhang
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
| | - Xiaohui Jiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yujia Ren
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Dawei Gao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Xiang Zhu
- Thermo Fisher ScientificShanghaiChina
| | - Björn Usadel
- Institute of Bio‐ and Geosciences, IBG‐4: Bioinformatics, CEPLAS, Forschungszentrum JülichJülichGermany
- Institute for Biological Data ScienceHeinrich Heine UniversityDüsseldorfGermany
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
| | - Weiwei Wen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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9
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Hubers N, Hagenbeek FA, Pool R, Déjean S, Harms AC, Roetman PJ, van Beijsterveldt CEM, Fanos V, Ehli EA, Vermeiren RRJM, Bartels M, Hottenga JJ, Hankemeier T, van Dongen J, Boomsma DI. Integrative multi-omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention-Deficit/Hyperactivity Disorder. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32955. [PMID: 37534875 DOI: 10.1002/ajmg.b.32955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The evolving field of multi-omics combines data and provides methods for simultaneous analysis across several omics levels. Here, we integrated genomics (transmitted and non-transmitted polygenic scores [PGSs]), epigenomics, and metabolomics data in a multi-omics framework to identify biomarkers for Attention-Deficit/Hyperactivity Disorder (ADHD) and investigated the connections among the three omics levels. We first trained single- and next multi-omics models to differentiate between cases and controls in 596 twins (cases = 14.8%) from the Netherlands Twin Register (NTR) demonstrating reasonable in-sample prediction through cross-validation. The multi-omics model selected 30 PGSs, 143 CpGs, and 90 metabolites. We confirmed previous associations of ADHD with glucocorticoid exposure and the transmembrane protein family TMEM, show that the DNA methylation of the MAD1L1 gene associated with ADHD has a relation with parental smoking behavior, and present novel findings including associations between indirect genetic effects and CpGs of the STAP2 gene. However, out-of-sample prediction in NTR participants (N = 258, cases = 14.3%) and in a clinical sample (N = 145, cases = 51%) did not perform well (range misclassification was [0.40, 0.57]). The results highlighted connections between omics levels, with the strongest connections between non-transmitted PGSs, CpGs, and amino acid levels and show that multi-omics designs considering interrelated omics levels can help unravel the complex biology underlying ADHD.
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Affiliation(s)
- Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219, University of Toulouse, CNRS, Toulouse, France
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Peter J Roetman
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, USA
| | - Robert R J M Vermeiren
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
- Youz, Parnassia Group, the Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
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10
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Zhan Y, Zhang J, Yang R, Deng Z, Chen S, Feng J, Wu J, Huang Q, Gu Y, Xie J. Blood glucose and lipids are associated with sarcoidosis: findings from observational and mendelian randomization studies. Respir Res 2024; 25:50. [PMID: 38254098 PMCID: PMC10804582 DOI: 10.1186/s12931-023-02663-4] [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: 11/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Several researches have demonstrated that patients with sarcoidosis accompanied with the abnormality in blood glucose and/or lipids, however, the causal relationship between them remains uncertain. To elucidate the potential association and causality of blood glucose and lipids with sarcoidosis, we conducted a propensity score matching (PSM)-based observational study combined with mendelian randomization (MR) analysis. METHODS All subjects in this study were retrospectively collected from Tongji Hospital during 2010 and 2023. 1:1 PSM was employed to control the potential confounders as appropriate. Univariable and multivariable logistic regression analyses were performed to estimate the associations of sarcoidosis with fasting glucose, high density lipoprotein cholesterol (HDLC), low density lipoprotein cholesterol (LDLC), total cholesterol (TC), and total triglyceride (TG). The further subtype analysis was also conducted. Afterwards, a bidirectional MR analysis based on public data deeply explored the causality among the 5 candidate traits and sarcoidosis, for which the inverse-variance weighted (IVW) method was utilized as the main inferring approach. RESULTS In the observational study, a total number of 756 subjects were enrolled, with 162 sarcoidosis patients and 594 non-sarcoidosis participants, while 160 pairs of subjects were matched after PSM. Multivariable logistic regression analysis indicated that HDLC (OR: 0.151; 95% CI: 0.056-0.408; P < 0.001) and TC (OR: 3.942; 95% CI: 2.644-5.877; P < 0.001) were strongly associated with sarcoidosis. Subtype analysis showed that low HDLC was independently correlated to risk of lesions in bronchus and lungs, and mediastinal lymph nodes, while high TC was to cervical lymph nodes. In MR analysis, high fasting glucose, low HDLC, and high TC were identified as the causal factors of sarcoidosis. CONCLUSION HDLC and TC had the potential to influence the risk of sarcoidosis, which could be regarded as predictors and may provide new diagnostic and therapeutic targets for sarcoidosis.
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Affiliation(s)
- Yuan Zhan
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jiaheng Zhang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ruonan Yang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhesong Deng
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Shanshan Chen
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jie Feng
- Department of Social Medicine and Health Management, School of Public Health, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jixing Wu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Qian Huang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yiya Gu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jungang Xie
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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11
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Daubney ER, D'Urso S, Cuellar-Partida G, Rajbhandari D, Peach E, de Guzman E, McArthur C, Rhodes A, Meyer J, Finfer S, Myburgh J, Cohen J, Schirra HJ, Venkatesh B, Evans DM. A Genome-Wide Association Study of Serum Metabolite Profiles in Septic Shock Patients. Crit Care Explor 2024; 6:e1030. [PMID: 38239409 PMCID: PMC10796137 DOI: 10.1097/cce.0000000000001030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
OBJECTIVES We sought to assess whether genetic associations with metabolite concentrations in septic shock patients could be used to identify pathways of potential importance for understanding sepsis pathophysiology. DESIGN Retrospective multicenter cohort studies of septic shock patients. SETTING All participants who were admitted to 27 participating hospital sites in three countries (Australia, New Zealand, and the United Kingdom) were eligible for inclusion. PATIENTS Adult, critically ill, mechanically ventilated patients with septic shock (n = 230) who were a subset of the Adjunctive Corticosteroid Treatment in Critically Ill Patients with Septic Shock trial (ClinicalTrials.gov number: NCT01448109). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A genome-wide association study was conducted for a range of serum metabolite levels for participants. Genome-wide significant associations (p ≤ 5 × 10-8) were found for the two major ketone bodies (3-hydroxybutyrate [rs2456680] and acetoacetate [rs2213037] and creatinine (rs6851961). One of these single-nucleotide polymorphisms (SNPs) (rs2213037) was located in the alcohol dehydrogenase cluster of genes, which code for enzymes related to the metabolism of acetoacetate and, therefore, presents a plausible association for this metabolite. None of the three SNPs showed strong associations with risk of sepsis, 28- or 90-day mortality, or Acute Physiology and Chronic Health Evaluation score (a measure of sepsis severity). CONCLUSIONS We suggest that the genetic associations with metabolites may reflect a starvation response rather than processes involved in sepsis pathophysiology. However, our results require further investigation and replication in both healthy and diseased cohorts including those of different ancestry.
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Affiliation(s)
- Emily R Daubney
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Shannon D'Urso
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | | | - Elizabeth Peach
- Frazer Institute, University of Queensland, Brisbane, QLD, Australia
| | - Erika de Guzman
- Australian Translational Genomics Centre, Queensland University of Technology, Brisbane, QLD, Australia
| | - Colin McArthur
- Department of Critical Care Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Andrew Rhodes
- Department of Adult Critical Care, St George's University Hospitals NHS Foundation Trust and St George's University of London, London, United Kingdom
| | - Jason Meyer
- The George Institute for Global Health, Sydney, NSW, Australia
- Intensive Care Unit, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Simon Finfer
- The George Institute for Global Health, Sydney, NSW, Australia
- School of Public Health, Imperial College London, London, United Kingdom
| | - John Myburgh
- The George Institute for Global Health, Sydney, NSW, Australia
- St George Hospital, Sydney, NSW, Australia
| | - Jeremy Cohen
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
- Intensive Care Unit, The Wesley Hospital, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Horst Joachim Schirra
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
- Griffith School of Environment and Science-Chemical Sciences, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
| | - Balasubramanian Venkatesh
- The George Institute for Global Health, Sydney, NSW, Australia
- Intensive Care Unit, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Intensive Care Unit, The Wesley Hospital, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Faculty of Health, University of New South Wales, Sydney, NSW, Australia
| | - David M Evans
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, University of Queensland, Brisbane, QLD, Australia
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
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12
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Drouard G, Hagenbeek FA, Whipp AM, Pool R, Hottenga JJ, Jansen R, Hubers N, Afonin A, Willemsen G, de Geus EJC, Ripatti S, Pirinen M, Kanninen KM, Boomsma DI, van Dongen J, Kaprio J. Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins. BMC Med 2023; 21:508. [PMID: 38129841 PMCID: PMC10740308 DOI: 10.1186/s12916-023-03198-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND The influence of genetics and environment on the association of the plasma proteome with body mass index (BMI) and changes in BMI remains underexplored, and the links to other omics in these associations remain to be investigated. We characterized protein-BMI trajectory associations in adolescents and adults and how these connect to other omics layers. METHODS Our study included two cohorts of longitudinally followed twins: FinnTwin12 (N = 651) and the Netherlands Twin Register (NTR) (N = 665). Follow-up comprised 4 BMI measurements over approximately 6 (NTR: 23-27 years old) to 10 years (FinnTwin12: 12-22 years old), with omics data collected at the last BMI measurement. BMI changes were calculated in latent growth curve models. Mixed-effects models were used to quantify the associations between the abundance of 439 plasma proteins with BMI at blood sampling and changes in BMI. In FinnTwin12, the sources of genetic and environmental variation underlying the protein abundances were quantified by twin models, as were the associations of proteins with BMI and BMI changes. In NTR, we investigated the association of gene expression of genes encoding proteins identified in FinnTwin12 with BMI and changes in BMI. We linked identified proteins and their coding genes to plasma metabolites and polygenic risk scores (PRS) applying mixed-effects models and correlation networks. RESULTS We identified 66 and 14 proteins associated with BMI at blood sampling and changes in BMI, respectively. The average heritability of these proteins was 35%. Of the 66 BMI-protein associations, 43 and 12 showed genetic and environmental correlations, respectively, including 8 proteins showing both. Similarly, we observed 7 and 3 genetic and environmental correlations between changes in BMI and protein abundance, respectively. S100A8 gene expression was associated with BMI at blood sampling, and the PRG4 and CFI genes were associated with BMI changes. Proteins showed strong connections with metabolites and PRSs, but we observed no multi-omics connections among gene expression and other omics layers. CONCLUSIONS Associations between the proteome and BMI trajectories are characterized by shared genetic, environmental, and metabolic etiologies. We observed few gene-protein pairs associated with BMI or changes in BMI at the proteome and transcriptome levels.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Fiona A Hagenbeek
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Alyce M Whipp
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Rick Jansen
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, The Netherlands
| | - Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Aleksei Afonin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
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13
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Fuller H, Zhu Y, Nicholas J, Chatelaine HA, Drzymalla EM, Sarvestani AK, Julián-Serrano S, Tahir UA, Sinnott-Armstrong N, Raffield LM, Rahnavard A, Hua X, Shutta KH, Darst BF. Metabolomic epidemiology offers insights into disease aetiology. Nat Metab 2023; 5:1656-1672. [PMID: 37872285 PMCID: PMC11164316 DOI: 10.1038/s42255-023-00903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Metabolomic epidemiology is the high-throughput study of the relationship between metabolites and health-related traits. This emerging and rapidly growing field has improved our understanding of disease aetiology and contributed to advances in precision medicine. As the field continues to develop, metabolomic epidemiology could lead to the discovery of diagnostic biomarkers predictive of disease risk, aiding in earlier disease detection and better prognosis. In this Review, we discuss key advances facilitated by the field of metabolomic epidemiology for a range of conditions, including cardiometabolic diseases, cancer, Alzheimer's disease and COVID-19, with a focus on potential clinical utility. Core principles in metabolomic epidemiology, including study design, causal inference methods and multi-omic integration, are briefly discussed. Future directions required for clinical translation of metabolomic epidemiology findings are summarized, emphasizing public health implications. Further work is needed to establish which metabolites reproducibly improve clinical risk prediction in diverse populations and are causally related to disease progression.
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Affiliation(s)
- Harriett Fuller
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yiwen Zhu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jayna Nicholas
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Haley A Chatelaine
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Emily M Drzymalla
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Afrand K Sarvestani
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | | | - Usman A Tahir
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Xinwei Hua
- Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Burcu F Darst
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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14
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Weinisch P, Raffler J, Römisch-Margl W, Arnold M, Mohney RP, Rist MJ, Prehn C, Skurk T, Hauner H, Daniel H, Suhre K, Kastenmüller G. The HuMet Repository: Watching human metabolism at work. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.550079. [PMID: 37609175 PMCID: PMC10441358 DOI: 10.1101/2023.08.08.550079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The human metabolism constantly responds to stimuli such as food intake, fasting, exercise, and stress, triggering adaptive biochemical processes across multiple metabolic pathways. To understand the role of these processes and disruptions thereof in health and disease, detailed documentation of healthy metabolic responses is needed but still scarce on a time-resolved metabolome-wide level. Here, we present the HuMet Repository, a web-based resource for exploring dynamic metabolic responses to six physiological challenges (exercise, 36 h fasting, oral glucose and lipid loads, mixed meal, cold stress) in healthy subjects. For building this resource, we integrated existing and newly derived metabolomics data measured in blood, urine, and breath samples of 15 young healthy men at up to 56 time points during the six highly standardized challenge tests conducted over four days. The data comprise 1.1 million data points acquired on multiple platforms with temporal profiles of 2,656 metabolites from a broad range of biochemical pathways. By embedding the dataset into an interactive web application, we enable users to easily access, search, filter, analyze, and visualize the time-resolved metabolomic readouts and derived results. Users can put metabolites into their larger context by identifying metabolites with similar trajectories or by visualizing metabolites within holistic metabolic networks to pinpoint pathways of interest. In three showcases, we outline the value of the repository for gaining biological insights and generating hypotheses by analyzing the wash-out of dietary markers, the complementarity of metabolomics platforms in dynamic versus cross-sectional data, and similarities and differences in systemic metabolic responses across challenges. With its comprehensive collection of time-resolved metabolomics data, the HuMet Repository, freely accessible at https://humet.org/, is a reference for normal, healthy responses to metabolic challenges in young males. It will enable researchers with and without computational expertise, to flexibly query the data for their own research into the dynamics of human metabolism.
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Affiliation(s)
- Patrick Weinisch
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Raffler
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Digital Medicine, University Hospital of Augsburg, Augsburg, Germany
| | - Werner Römisch-Margl
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | | | - Manuela J. Rist
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Cornelia Prehn
- Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Skurk
- ZIEL Institute for Food and Health, Core Facility Human Studies, Technical University of Munich, Freising, Germany
- Else Kröner Fresenius Center of Nutritional Medicine, Department of Food and Nutrition, Technical University of Munich, Freising, Germany
| | - Hans Hauner
- Else Kröner Fresenius Center of Nutritional Medicine, Department of Food and Nutrition, Technical University of Munich, Freising, Germany
- Institute for Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Hannelore Daniel
- Department of Food and Nutrition, Technical University of Munich, Freising, Germany
| | - Karsten Suhre
- Department of Biophysics and Physiology, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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15
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Drouard G, Hagenbeek FA, Whipp A, Pool R, Hottenga JJ, Jansen R, Hubers N, Afonin A, Willemsen G, de Geus EJC, Ripatti S, Pirinen M, Kanninen KM, Boomsma DI, van Dongen J, Kaprio J. Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291995. [PMID: 37425750 PMCID: PMC10327285 DOI: 10.1101/2023.06.28.23291995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Background The influence of genetics and environment on the association of the plasma proteome with body mass index (BMI) and changes in BMI remain underexplored, and the links to other omics in these associations remain to be investigated. We characterized protein-BMI trajectory associations in adolescents and adults and how these connect to other omics layers. Methods Our study included two cohorts of longitudinally followed twins: FinnTwin12 (N=651) and the Netherlands Twin Register (NTR) (N=665). Follow-up comprised four BMI measurements over approximately 6 (NTR: 23-27 years old) to 10 years (FinnTwin12: 12-22 years old), with omics data collected at the last BMI measurement. BMI changes were calculated using latent growth curve models. Mixed-effects models were used to quantify the associations between the abundance of 439 plasma proteins with BMI at blood sampling and changes in BMI. The sources of genetic and environmental variation underlying the protein abundances were quantified using twin models, as were the associations of proteins with BMI and BMI changes. In NTR, we investigated the association of gene expression of genes encoding proteins identified in FinnTwin12 with BMI and changes in BMI. We linked identified proteins and their coding genes to plasma metabolites and polygenic risk scores (PRS) using mixed-effect models and correlation networks. Results We identified 66 and 14 proteins associated with BMI at blood sampling and changes in BMI, respectively. The average heritability of these proteins was 35%. Of the 66 BMI-protein associations, 43 and 12 showed genetic and environmental correlations, respectively, including 8 proteins showing both. Similarly, we observed 6 and 4 genetic and environmental correlations between changes in BMI and protein abundance, respectively. S100A8 gene expression was associated with BMI at blood sampling, and the PRG4 and CFI genes were associated with BMI changes. Proteins showed strong connections with many metabolites and PRSs, but we observed no multi-omics connections among gene expression and other omics layers. Conclusions Associations between the proteome and BMI trajectories are characterized by shared genetic, environmental, and metabolic etiologies. We observed few gene-protein pairs associated with BMI or changes in BMI at the proteome and transcriptome levels.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Fiona A. Hagenbeek
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Alyce Whipp
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Rick Jansen
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, The Netherlands
| | - Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Aleksei Afonin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - BIOS Consortium
- Biobank-based Integrative Omics Study Consortium. Lists of authors and their affiliations appear in the supplementary material (see Additional file 1)
| | | | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Eco J. C. de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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16
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Hagenbeek FA, Hirzinger JS, Breunig S, Bruins S, Kuznetsov DV, Schut K, Odintsova VV, Boomsma DI. Maximizing the value of twin studies in health and behaviour. Nat Hum Behav 2023:10.1038/s41562-023-01609-6. [PMID: 37188734 DOI: 10.1038/s41562-023-01609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
In the classical twin design, researchers compare trait resemblance in cohorts of identical and non-identical twins to understand how genetic and environmental factors correlate with resemblance in behaviour and other phenotypes. The twin design is also a valuable tool for studying causality, intergenerational transmission, and gene-environment correlation and interaction. Here we review recent developments in twin studies, recent results from twin studies of new phenotypes and recent insights into twinning. We ask whether the results of existing twin studies are representative of the general population and of global diversity, and we conclude that stronger efforts to increase representativeness are needed. We provide an updated overview of twin concordance and discordance for major diseases and mental disorders, which conveys a crucial message: genetic influences are not as deterministic as many believe. This has important implications for public understanding of genetic risk prediction tools, as the accuracy of genetic predictions can never exceed identical twin concordance rates.
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Affiliation(s)
- Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.
| | - Jana S Hirzinger
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Sophie Breunig
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Psychology & Neuroscience, University of Colorado Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Susanne Bruins
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dmitry V Kuznetsov
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Faculty of Sociology, Bielefeld University, Bielefeld, Germany
| | - Kirsten Schut
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Nightingale Health Plc, Helsinki, Finland
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Department of Psychiatry, University Medical Center of Groningen, University of Groningen, Groningen, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands.
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17
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Tian J, Zhu X, Wu H, Wang Y, Hu X. Serum metabolic profile and metabolome genome-wide association study in chicken. J Anim Sci Biotechnol 2023; 14:69. [PMID: 37138301 PMCID: PMC10158329 DOI: 10.1186/s40104-023-00868-7] [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: 12/12/2022] [Accepted: 03/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. RESULTS Here, comprehensive metabolome detection was performed using non-targeted LC-MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. CONCLUSIONS We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hanyu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
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18
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Jain P, Yates M, de Celis CR, Drineas P, Jahanshad N, Thompson P, Paschou P. Multiomic approach and Mendelian randomization analysis identify causal associations between blood biomarkers and subcortical brain structure volumes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287968. [PMID: 37066330 PMCID: PMC10104218 DOI: 10.1101/2023.03.30.23287968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Alterations in subcortical brain structure volumes have been found to be associated with several neurodegenerative and psychiatric disorders. At the same time, genome-wide association studies (GWAS) have identified numerous common variants associated with brain structure. In this study, we integrate these findings, aiming to identify proteins, metabolites, or microbes that have a putative causal association with subcortical brain structure volumes via a two-sample Mendelian randomization approach. This method uses genetic variants as instrument variables to identify potentially causal associations between an exposure and an outcome. The exposure data that we analyzed comprised genetic associations for 2,994 plasma proteins, 237 metabolites, and 103 microbial genera. The outcome data included GWAS data for seven subcortical brain structure volumes including accumbens, amygdala, caudate, hippocampus, pallidum, putamen, and thalamus. Eleven proteins and six metabolites were found to have a significant association with subcortical structure volumes. We found causal associations between amygdala volume and granzyme A as well as association between accumbens volume and plasma protease c1 inhibitor. Among metabolites, urate had the strongest association with thalamic volume. No significant associations were detected between the microbial genera and subcortical brain structure volumes. We also observed significant enrichment for biological processes such as proteolysis, regulation of the endoplasmic reticulum apoptotic signaling pathway, and negative regulation of DNA binding. Our findings provide insights to the mechanisms through which brain volumes may be affected in the pathogenesis of neurodevelopmental and psychiatric disorders and point to potential treatment targets for disorders that are associated with subcortical brain structure volumes.
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Affiliation(s)
- Pritesh Jain
- Department of Biological Sciences, Purdue University
| | - Madison Yates
- Department of Biological Sciences, Purdue University
| | | | | | - Neda Jahanshad
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of South California
| | - Paul Thompson
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of South California
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19
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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20
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Elsea SH, Posey JE. Metabolic individuality: Limitations, challenges, and potential for clinical utility. Cell Metab 2023; 35:233-235. [PMID: 36754017 DOI: 10.1016/j.cmet.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In Nature Medicine, Surendran and colleagues recently reported the analysis of human plasma metabolomic data for 913 metabolites in ∼20,000 individuals, identifying 2,599 metabolite-genetic variant associations and >400 metabolite signatures comprised of jointly regulated metabolites. This extensive atlas of variant-metabolite relationships reveals novel genomic mechanisms driving metabolic phenotypes.
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Affiliation(s)
- Sarah H Elsea
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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21
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Yang M, Xu J, Zhang F, Luo P, Xu K, Feng R, Xu P. Large-Scale Genetic Correlation Analysis between Spondyloarthritis and Human Blood Metabolites. J Clin Med 2023; 12:jcm12031201. [PMID: 36769847 PMCID: PMC9917834 DOI: 10.3390/jcm12031201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/05/2023] Open
Abstract
The aim was to study the genetic correlation and causal relationship between spondyloarthritis (SpA) and blood metabolites based on the large-scale genome-wide association study (GWAS) summary data. The GWAS summary data (3966 SpA and 448,298 control cases) of SpA were from the UK Biobank, and the GWAS summary data (486 blood metabolites) of human blood metabolites were from a published study. First, the genetic correlation between SpA and blood metabolites was analyzed by linkage disequilibrium score (LDSC) regression. Next, we used Mendelian randomization (MR) analysis to perform access causal relationship between SpA and blood metabolites. Random effects inverse variance weighted (IVW) was the main analysis method, and the MR Egger, weighted median, simple mode, and weighted mode were supplementary methods. The MR analysis results were dominated by the random effects IVW. The Cochran's Q statistic (MR-IVW) and Rucker's Q statistic (MR Egger) were used to check heterogeneity. MR Egger and MR pleiotropy residual sum and outlier (MR-PRESSO) were used to check horizontal pleiotropy. The MR-PRESSO was also used to check outliers. The "leave-one-out" analysis was used to assess whether the MR analysis results were affected by a single SNP and thus test the robustness of the MR results. Finally, we identified seven blood metabolites that are genetically related to SpA: X-10395 (correlation coefficient = -0.546, p = 0.025), pantothenate (correlation coefficient = -0.565, p = 0.038), caprylate (correlation coefficient = -0.333, p = 0.037), pelargonate (correlation coefficient = -0.339, p = 0.047), X-11317 (correlation coefficient = -0.350, p = 0.038), X-12510 (correlation coefficient = -0.399, p = 0.034), and X-13859 (Correlation coefficient = -0.458, p = 0.015). Among them, X-10395 had a positive genetic causal relationship with SpA (p = 0.014, OR = 1.011). The blood metabolites that have genetic correlation and causal relationship with SpA found in this study provide a new idea for the study of the pathogenesis of SpA and the determination of diagnostic indicators.
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Affiliation(s)
- Mingyi Yang
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an 710054, China
| | - Jiawen Xu
- Orthopedic Research Institute, Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China
| | - Pan Luo
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an 710054, China
| | - Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an 710054, China
- Correspondence:
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22
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Iwasaki T, Kamatani Y, Sonomura K, Kawaguchi S, Kawaguchi T, Takahashi M, Ohmura K, Sato TA, Matsuda F. Genetic influences on human blood metabolites in the Japanese population. iScience 2023; 26:105738. [PMID: 36582826 PMCID: PMC9792902 DOI: 10.1016/j.isci.2022.105738] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/08/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
An increase in ethnic diversity in genetic studies has the potential to provide unprecedented insights into how genetic variations influence human phenotypes. In this study, we conducted a quantitative trait locus (QTL) analysis of 121 metabolites measured using gas chromatography-mass spectrometry with plasma samples from 4,888 Japanese individuals. We found 60 metabolite-gene associations, of which 13 have not been previously reported. Meta-analyses with another Japanese and a European study identified six and two additional unreported loci, respectively. Genetic variants influencing metabolite levels were more enriched in protein-coding regions than in the regulatory regions while being associated with the risk of various diseases. Finally, we identified a signature of strong negative selection for uric acid ( S ˆ = -1.53, p = 6.2 × 10-18). Our study expanded the knowledge of genetic influences on human blood metabolites, providing valuable insights into their physiological, pathological, and selective properties.
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Affiliation(s)
- Takeshi Iwasaki
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan.,Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Yoichiro Kamatani
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kazuhiro Sonomura
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan.,Life Science Research Center, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Shuji Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Taka-Aki Sato
- Life Science Research Center, Shimadzu Corporation, Kyoto 604-8511, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
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23
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Zandl-Lang M, Plecko B, Köfeler H. Lipidomics-Paving the Road towards Better Insight and Precision Medicine in Rare Metabolic Diseases. Int J Mol Sci 2023; 24:ijms24021709. [PMID: 36675224 PMCID: PMC9866746 DOI: 10.3390/ijms24021709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Even though the application of Next-Generation Sequencing (NGS) has significantly facilitated the identification of disease-associated mutations, the diagnostic rate of rare diseases is still below 50%. This causes a diagnostic odyssey and prevents specific treatment, as well as genetic counseling for further family planning. Increasing the diagnostic rate and reducing the time to diagnosis in children with unclear disease are crucial for a better patient outcome and improvement of quality of life. In many cases, NGS reveals variants of unknown significance (VUS) that need further investigations. The delineation of novel (lipid) biomarkers is not only crucial to prove the pathogenicity of VUS, but provides surrogate parameters for the monitoring of disease progression and therapeutic interventions. Lipids are essential organic compounds in living organisms, serving as building blocks for cellular membranes, energy storage and signaling molecules. Among other disorders, an imbalance in lipid homeostasis can lead to chronic inflammation, vascular dysfunction and neurodegenerative diseases. Therefore, analyzing lipids in biological samples provides great insight into the underlying functional role of lipids in healthy and disease statuses. The method of choice for lipid analysis and/or huge assemblies of lipids (=lipidome) is mass spectrometry due to its high sensitivity and specificity. Due to the inherent chemical complexity of the lipidome and the consequent challenges associated with analyzing it, progress in the field of lipidomics has lagged behind other omics disciplines. However, compared to the previous decade, the output of publications on lipidomics has increased more than 17-fold within the last decade and has, therefore, become one of the fastest-growing research fields. Combining multiple omics approaches will provide a unique and efficient tool for determining pathogenicity of VUS at the functional level, and thereby identifying rare, as well as novel, genetic disorders by molecular techniques and biochemical analyses.
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Affiliation(s)
- Martina Zandl-Lang
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Barbara Plecko
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Harald Köfeler
- Core Facility Mass Spectrometry, ZMF, Medical University of Graz, 8036 Graz, Austria
- Correspondence:
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24
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Molecular Landscape of Tourette's Disorder. Int J Mol Sci 2023; 24:ijms24021428. [PMID: 36674940 PMCID: PMC9865021 DOI: 10.3390/ijms24021428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023] Open
Abstract
Tourette's disorder (TD) is a highly heritable childhood-onset neurodevelopmental disorder and is caused by a complex interplay of multiple genetic and environmental factors. Yet, the molecular mechanisms underlying the disorder remain largely elusive. In this study, we used the available omics data to compile a list of TD candidate genes, and we subsequently conducted tissue/cell type specificity and functional enrichment analyses of this list. Using genomic data, we also investigated genetic sharing between TD and blood and cerebrospinal fluid (CSF) metabolite levels. Lastly, we built a molecular landscape of TD through integrating the results from these analyses with an extensive literature search to identify the interactions between the TD candidate genes/proteins and metabolites. We found evidence for an enriched expression of the TD candidate genes in four brain regions and the pituitary. The functional enrichment analyses implicated two pathways ('cAMP-mediated signaling' and 'Endocannabinoid Neuronal Synapse Pathway') and multiple biological functions related to brain development and synaptic transmission in TD etiology. Furthermore, we found genetic sharing between TD and the blood and CSF levels of 39 metabolites. The landscape of TD not only provides insights into the (altered) molecular processes that underlie the disease but, through the identification of potential drug targets (such as FLT3, NAALAD2, CX3CL1-CX3CR1, OPRM1, and HRH2), it also yields clues for developing novel TD treatments.
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25
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Chen Y, Lu T, Pettersson-Kymmer U, Stewart ID, Butler-Laporte G, Nakanishi T, Cerani A, Liang KYH, Yoshiji S, Willett JDS, Su CY, Raina P, Greenwood CMT, Farjoun Y, Forgetta V, Langenberg C, Zhou S, Ohlsson C, Richards JB. Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases. Nat Genet 2023; 55:44-53. [PMID: 36635386 PMCID: PMC7614162 DOI: 10.1038/s41588-022-01270-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 11/18/2022] [Indexed: 01/14/2023]
Abstract
Metabolic processes can influence disease risk and provide therapeutic targets. By conducting genome-wide association studies of 1,091 blood metabolites and 309 metabolite ratios, we identified associations with 690 metabolites at 248 loci and associations with 143 metabolite ratios at 69 loci. Integrating metabolite-gene and gene expression information identified 94 effector genes for 109 metabolites and 48 metabolite ratios. Using Mendelian randomization (MR), we identified 22 metabolites and 20 metabolite ratios having estimated causal effect on 12 traits and diseases, including orotate for estimated bone mineral density, α-hydroxyisovalerate for body mass index and ergothioneine for inflammatory bowel disease and asthma. We further measured the orotate level in a separate cohort and demonstrated that, consistent with MR, orotate levels were positively associated with incident hip fractures. This study provides a valuable resource describing the genetic architecture of metabolites and delivers insights into their roles in common diseases, thereby offering opportunities for therapeutic targets.
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Affiliation(s)
- Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | | | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Agustin Cerani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Julian Daniel Sunday Willett
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Computer Science, McGill University, Montreal, Quebec, Canada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- McMaster Institute for Research on Aging, McMaster University, Hamilton, Ontario, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Fulcrum Genomics, Boulder, CO, USA
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre of Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- 5 Prime Sciences Inc, Montreal, Quebec, Canada.
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada.
- Department of Medicine, McGill University, Montreal, Quebec, Canada.
- Department of Twin Research, King's College London, London, UK.
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26
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Haj AK, Hasan H, Raife TJ. Heritability of Protein and Metabolite Biomarkers Associated with COVID-19 Severity: A Metabolomics and Proteomics Analysis. Biomolecules 2022; 13:46. [PMID: 36671431 PMCID: PMC9855380 DOI: 10.3390/biom13010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Prior studies have characterized protein and metabolite changes associated with SARS-CoV-2 infection; we hypothesized that these biomarkers may be part of heritable metabolic pathways in erythrocytes. METHODS Using a twin study of erythrocyte protein and metabolite levels, we describe the heritability of, and correlations among, previously identified biomarkers that correlate with COVID-19 severity. We used gene ontology and pathway enrichment analysis tools to identify pathways and biological processes enriched among these biomarkers. RESULTS Many COVID-19 biomarkers are highly heritable in erythrocytes. Among heritable metabolites downregulated in COVID-19, metabolites involved in amino acid metabolism and biosynthesis are enriched. Specific amino acid metabolism pathways (valine, leucine, and isoleucine biosynthesis; glycine, serine, and threonine metabolism; and arginine biosynthesis) are heritable in erythrocytes. CONCLUSIONS Metabolic pathways downregulated in COVID-19, particularly amino acid biosynthesis and metabolism pathways, are heritable in erythrocytes. This finding suggests that a component of the variation in COVID-19 severity may be the result of phenotypic variation in heritable metabolic pathways; future studies will be necessary to determine whether individual variation in amino acid metabolism pathways correlates with heritable outcomes of COVID-19.
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Affiliation(s)
| | | | - Thomas J. Raife
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 3170 UW Medical Foundation Centennial Building (MFCB), Madison, WI 53705-2281, USA
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27
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Wu Q, Li J, Zhu J, Sun X, He D, Li J, Cheng Z, Zhang X, Xu Y, Chen Q, Zhu Y, Lai M. Gamma-glutamyl-leucine levels are causally associated with elevated cardio-metabolic risks. Front Nutr 2022; 9:936220. [PMID: 36505257 PMCID: PMC9729530 DOI: 10.3389/fnut.2022.936220] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022] Open
Abstract
Objective Gamma-glutamyl dipeptides are bioactive peptides involved in inflammation, oxidative stress, and glucose regulation. Gamma-glutamyl-leucine (Gamma-Glu-Leu) has been extensively reported to be associated with the risk of cardio-metabolic diseases, such as obesity, metabolic syndrome, and type 2 diabetes. However, the causality remains to be uncovered. The aim of this study was to explore the causal-effect relationships between Gamma-Glu-Leu and metabolic risk. Materials and methods In this study, 1,289 subjects were included from a cross-sectional survey on metabolic syndrome (MetS) in eastern China. Serum Gamma-Glu-Leu levels were measured by untargeted metabolomics. Using linear regressions, a two-stage genome-wide association study (GWAS) for Gamma-Glu-Leu was conducted to seek its instrumental single nucleotide polymorphisms (SNPs). One-sample Mendelian randomization (MR) analyses were performed to evaluate the causality between Gamma-Glu-Leu and the metabolic risk. Results Four SNPs are associated with serum Gamma-Glu-Leu levels, including rs12476238, rs56146133, rs2479714, and rs12229654. Out of them, rs12476238 exhibits the strongest association (Beta = -0.38, S.E. = 0.07 in discovery stage, Beta = -0.29, S.E. = 0.14 in validation stage, combined P-value = 1.04 × 10-8). Each of the four SNPs has a nominal association with at least one metabolic risk factor. Both rs12229654 and rs56146133 are associated with body mass index, waist circumference (WC), the ratio of WC to hip circumference, blood pressure, and triglyceride (5 × 10-5 < P < 0.05). rs56146133 also has nominal associations with fasting insulin, glucose, and insulin resistance index (5 × 10-5 < P < 0.05). Using the four SNPs serving as the instrumental SNPs of Gamma-Glu-Leu, the MR analyses revealed that higher Gamma-Glu-Leu levels are causally associated with elevated risks of multiple cardio-metabolic factors except for high-density lipoprotein cholesterol and low-density lipoprotein cholesterol (P > 0.05). Conclusion Four SNPs (rs12476238, rs56146133, rs2479714, and rs12229654) may regulate the levels of serum Gamma-Glu-Leu. Higher Gamma-Glu-Leu levels are causally linked to cardio-metabolic risks. Future prospective studies on Gamma-Glu-Leu are required to explain its role in metabolic disorders.
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Affiliation(s)
- Qiong Wu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Epidemiology and Biostatistics, School of Public Health, Hangzhou Normal University, Hangzhou, China
| | - Jiankang Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Jinghan Zhu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaohui Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Di He
- Department of Epidemiology and Biostatistics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Li
- Department of Epidemiology and Biostatistics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zongxue Cheng
- Department of Epidemiology and Biostatistics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuhui Zhang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China,Affiliated Hangzhou Center of Disease Control and Prevention, School of Public Health, Zhejiang University, Hangzhou, China
| | - Yuying Xu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qing Chen
- Zhejiang Provincial Centers for Disease Control and Prevention, Hangzhou, China,*Correspondence: Qing Chen,
| | - Yimin Zhu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Department of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Cancer Center, Zhejiang University, Hangzhou, China,Yimin Zhu,
| | - Maode Lai
- Key Laboratory of Disease Proteomics of Zhejiang Province, Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, China,State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Maode Lai,
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28
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Misganaw B, Yang R, Gautam A, Muhie S, Mellon SH, Wolkowitz OM, Ressler KJ, Doyle FJ, Marmar CR, Jett M, Hammamieh R. The Genetic Basis for the Increased Prevalence of Metabolic Syndrome among Post-Traumatic Stress Disorder Patients. Int J Mol Sci 2022; 23:12504. [PMID: 36293361 PMCID: PMC9604263 DOI: 10.3390/ijms232012504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Post-traumatic stress disorder (PTSD) is a highly debilitating psychiatric disorder that can be triggered by exposure to extreme trauma. Even if PTSD is primarily a psychiatric condition, it is also characterized by adverse somatic comorbidities. One illness commonly co-occurring with PTSD is Metabolic syndrome (MetS), which is defined by a set of health risk/resilience factors including obesity, elevated blood pressure, lower high-density lipoprotein cholesterol, higher low-density lipoprotein cholesterol, higher triglycerides, higher fasting blood glucose and insulin resistance. Here, phenotypic association between PTSD and components of MetS are tested on a military veteran cohort comprising chronic PTSD presentation (n = 310, 47% cases, 83% male). Consistent with previous observations, we found significant phenotypic correlation between the various components of MetS and PTSD severity scores. To examine if this observed symptom correlations stem from a shared genetic background, we conducted genetic correlation analysis using summary statistics data from large-scale genetic studies. Our results show robust positive genetic correlation between PTSD and MetS (rg[SE] = 0.33 [0.056], p = 4.74E-09), and obesity-related components of MetS (rg = 0.25, SE = 0.05, p = 6.4E-08). Prioritizing genomic regions with larger local genetic correlation implicate three significant loci. Overall, these findings show significant genetic overlap between PTSD and MetS, which may in part account for the markedly increased occurrence of MetS among PTSD patients.
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Affiliation(s)
- Burook Misganaw
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Vysnova Partners, Inc., Landover, MD 20785, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Seid Muhie
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Geneva Foundation, Silver Spring, MD 20910, USA
| | - Synthia H. Mellon
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Owen M. Wolkowitz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
| | - Kerry J. Ressler
- McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Francis J. Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02134, USA
| | - Charles R. Marmar
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marti Jett
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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Dijk W, Di Filippo M, Kooijman S, van Eenige R, Rimbert A, Caillaud A, Thedrez A, Arnaud L, Pronk A, Garçon D, Sotin T, Lindenbaum P, Ozcariz Garcia E, Pais de Barros JP, Duvillard L, Si-Tayeb K, Amigo N, Le Questel JY, Rensen PC, Le May C, Moulin P, Cariou B. Identification of a Gain-of-Function LIPC Variant as a Novel Cause of Familial Combined Hypocholesterolemia. Circulation 2022; 146:724-739. [PMID: 35899625 PMCID: PMC9439636 DOI: 10.1161/circulationaha.121.057978] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Atherosclerotic cardiovascular disease is the main cause of mortality worldwide and is strongly influenced by circulating low-density lipoprotein (LDL) cholesterol levels. Only a few genes causally related to plasma LDL cholesterol levels have been identified so far, and only 1 gene, ANGPTL3, has been causally related to combined hypocholesterolemia. Here, our aim was to elucidate the genetic origin of an unexplained combined hypocholesterolemia inherited in 4 generations of a French family. METHODS Using next-generation sequencing, we identified a novel dominant rare variant in the LIPC gene, encoding for hepatic lipase, which cosegregates with the phenotype. We characterized the impact of this LIPC-E97G variant on circulating lipid and lipoprotein levels in family members using nuclear magnetic resonance-based lipoprotein profiling and lipidomics. To uncover the mechanisms underlying the combined hypocholesterolemia, we used protein homology modeling, measured triglyceride lipase and phospholipase activities in cell culture, and studied the phenotype of APOE*3.Leiden.CETP mice after LIPC-E97G overexpression. RESULTS Family members carrying the LIPC-E97G variant had very low circulating levels of LDL cholesterol and high-density lipoprotein cholesterol, LDL particle numbers, and phospholipids. The lysophospholipids/phospholipids ratio was increased in plasma of LIPC-E97G carriers, suggestive of an increased lipolytic activity on phospholipids. In vitro and in vivo studies confirmed that the LIPC-E97G variant specifically increases the phospholipase activity of hepatic lipase through modification of an evolutionarily conserved motif that determines substrate access to the hepatic lipase catalytic site. Mice overexpressing human LIPC-E97G recapitulated the combined hypocholesterolemic phenotype of the family and demonstrated that the increased phospholipase activity promotes catabolism of triglyceride-rich lipoproteins by different extrahepatic tissues but not the liver. CONCLUSIONS We identified and characterized a novel rare variant in the LIPC gene in a family who presents with dominant familial combined hypocholesterolemia. This gain-of-function variant makes LIPC the second identified gene, after ANGPTL3, causally involved in familial combined hypocholesterolemia. Our mechanistic data highlight the critical role of hepatic lipase phospholipase activity in LDL cholesterol homeostasis and suggest a new LDL clearance mechanism.
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Affiliation(s)
- Wieneke Dijk
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Mathilde Di Filippo
- UF Dyslipidémies, Service de Biochimie et de Biologie Moléculaire, Laboratoire de Biologie Médicale MultiStites, Hospices Civils de Lyon, Bron, France (M.D.F.).,CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France (M.D.F., P.M.)
| | - Sander Kooijman
- Department of Medicine, Division of Endocrinology and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands (S.K., R.v.E., A.P., P.C.N.R.)
| | - Robin van Eenige
- Department of Medicine, Division of Endocrinology and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands (S.K., R.v.E., A.P., P.C.N.R.)
| | - Antoine Rimbert
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Amandine Caillaud
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Aurélie Thedrez
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Lucie Arnaud
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Amanda Pronk
- Department of Medicine, Division of Endocrinology and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands (S.K., R.v.E., A.P., P.C.N.R.)
| | - Damien Garçon
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Thibaud Sotin
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Pierre Lindenbaum
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | | | - Jean-Paul Pais de Barros
- Lipidomic Platform, INSERM UMR1231, Université de Bourgogne Franche-Comté, Dijon, France (J.-P.P.d.B.)
| | - Laurence Duvillard
- University of Burgundy, INSERM LNC UMR1231, Dijon, France (L.D.).,CHU Dijon, Department of Biochemistry, Dijon, France (L.D.)
| | - Karim Si-Tayeb
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Nuria Amigo
- Biosfer Teslab, Reus, Spain (E.O.G., N.A.).,Department of Basic Medical Sciences, Rovira I Virgili University, IISPV, CIBERDEM, Reus, Spain (N.A.)
| | | | - Patrick C.N. Rensen
- Department of Medicine, Division of Endocrinology and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands (S.K., R.v.E., A.P., P.C.N.R.)
| | - Cédric Le May
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
| | - Philippe Moulin
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France (M.D.F., P.M.).,Fédération d’endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Hospices Civils de Lyon, Bron, France (P.M.)
| | - Bertrand Cariou
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, France (W.D., A.R., A.C., A.T., L.A., D.G., T.S., P.L., K.S.-T., C.L.M., B.C.)
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Whole Exome Sequencing Enhanced Imputation Identifies 85 Metabolite Associations in the Alpine CHRIS Cohort. Metabolites 2022; 12:metabo12070604. [PMID: 35888728 PMCID: PMC9320943 DOI: 10.3390/metabo12070604] [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: 05/11/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Metabolites are intermediates or end products of biochemical processes involved in both health and disease. Here, we take advantage of the well-characterized Cooperative Health Research in South Tyrol (CHRIS) study to perform an exome-wide association study (ExWAS) on absolute concentrations of 175 metabolites in 3294 individuals. To increase power, we imputed the identified variants into an additional 2211 genotyped individuals of CHRIS. In the resulting dataset of 5505 individuals, we identified 85 single-variant genetic associations, of which 39 have not been reported previously. Fifteen associations emerged at ten variants with >5-fold enrichment in CHRIS compared to non-Finnish Europeans reported in the gnomAD database. For example, the CHRIS-enriched ETFDH stop gain variant p.Trp286Ter (rs1235904433-hexanoylcarnitine) and the MCCC2 stop lost variant p.Ter564GlnextTer3 (rs751970792-carnitine) have been found in patients with glutaric acidemia type II and 3-methylcrotonylglycinuria, respectively, but the loci have not been associated with the respective metabolites in a genome-wide association study (GWAS) previously. We further identified three gene-trait associations, where multiple rare variants contribute to the signal. These results not only provide further evidence for previously described associations, but also describe novel genes and mechanisms for diseases and disease-related traits.
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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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mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights. Metabolites 2022; 12:metabo12060526. [PMID: 35736459 PMCID: PMC9230867 DOI: 10.3390/metabo12060526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022] Open
Abstract
Tens of thousands of single-nucleotide polymorphisms (SNPs) have been identified to be significantly associated with metabolite abundance in over 65 genome-wide association studies with metabolomics (mGWAS) to date. Obtaining mechanistic or functional insights from these associations for translational applications has become a key research area in the mGWAS community. Here, we introduce mGWAS-Explorer, a user-friendly web-based platform to help connect SNPs, metabolites, genes, and their known disease associations via powerful network visual analytics. The application of the mGWAS-Explorer was demonstrated using a COVID-19 and a type 2 diabetes case studies.
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Heritability of Urinary Amines, Organic Acids, and Steroid Hormones in Children. Metabolites 2022; 12:metabo12060474. [PMID: 35736407 PMCID: PMC9228478 DOI: 10.3390/metabo12060474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Variation in metabolite levels reflects individual differences in genetic and environmental factors. Here, we investigated the role of these factors in urinary metabolomics data in children. We examined the effects of sex and age on 86 metabolites, as measured on three metabolomics platforms that target amines, organic acids, and steroid hormones. Next, we estimated their heritability in a twin cohort of 1300 twins (age range: 5.7–12.9 years). We observed associations between age and 50 metabolites and between sex and 21 metabolites. The monozygotic (MZ) and dizygotic (DZ) correlations for the urinary metabolites indicated a role for non-additive genetic factors for 50 amines, 13 organic acids, and 6 steroids. The average broad-sense heritability for these amines, organic acids, and steroids was 0.49 (range: 0.25–0.64), 0.50 (range: 0.33–0.62), and 0.64 (range: 0.43–0.81), respectively. For 6 amines, 7 organic acids, and 4 steroids the twin correlations indicated a role for shared environmental factors and the average narrow-sense heritability was 0.50 (range: 0.37–0.68), 0.50 (range; 0.23–0.61), and 0.47 (range: 0.32–0.70) for these amines, organic acids, and steroids. We conclude that urinary metabolites in children have substantial heritability, with similar estimates for amines and organic acids, and higher estimates for steroid hormones.
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Choudhury A, Brandenburg JT, Chikowore T, Sengupta D, Boua PR, Crowther NJ, Agongo G, Asiki G, Gómez-Olivé FX, Kisiangani I, Maimela E, Masemola-Maphutha M, Micklesfield LK, Nonterah EA, Norris SA, Sorgho H, Tinto H, Tollman S, Graham SE, Willer CJ, Hazelhurst S, Ramsay M. Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits. Nat Commun 2022; 13:2578. [PMID: 35546142 PMCID: PMC9095599 DOI: 10.1038/s41467-022-30098-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/18/2022] [Indexed: 12/30/2022] Open
Abstract
Genetic associations for lipid traits have identified hundreds of variants with clear differences across European, Asian and African studies. Based on a sub-Saharan-African GWAS for lipid traits in the population cross-sectional AWI-Gen cohort (N = 10,603) we report a novel LDL-C association in the GATB region (P-value=1.56 × 10−8). Meta-analysis with four other African cohorts (N = 23,718) provides supporting evidence for the LDL-C association with the GATB/FHIP1A region and identifies a novel triglyceride association signal close to the FHIT gene (P-value =2.66 × 10−8). Our data enable fine-mapping of several well-known lipid-trait loci including LDLR, PMFBP1 and LPA. The transferability of signals detected in two large global studies (GLGC and PAGE) consistently improves with an increase in the size of the African replication cohort. Polygenic risk score analysis shows increased predictive accuracy for LDL-C levels with the narrowing of genetic distance between the discovery dataset and our cohort. Novel discovery is enhanced with the inclusion of African data. Genetic associations and polygenic scores for lipid traits have low transferability to African individuals. Here, the authors perform a large sub-Sarahan African lipid GWAS and find that larger datasets and better global representation in discovery GWAS help to bridge this gap.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,South African Medical Research Council/University of the Witwatersrand Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwende Romuald Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santè, Nanoro, Burkina Faso
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.,C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Eric Maimela
- Department of Public Health, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Matshane Masemola-Maphutha
- Department of Pathology and Medical Sciences, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Lisa K Micklesfield
- South African Medical Research Council/University of the Witwatersrand Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Shane A Norris
- South African Medical Research Council/University of the Witwatersrand Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santè, Nanoro, Burkina Faso
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santè, Nanoro, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48019, USA
| | | | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Genome-wide association and Mendelian randomization study of blood copper levels and 213 deep phenotypes in humans. Commun Biol 2022; 5:405. [PMID: 35501403 PMCID: PMC9061855 DOI: 10.1038/s42003-022-03351-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/10/2022] [Indexed: 11/29/2022] Open
Abstract
Metal elements are present in the human body, and their levels in the blood have important impacts on health. In this study, 2488 Chinese individuals were included in a genome-wide association study of 21 serum metal levels, with approximately 179,000 East Asian individuals in a bidirectional two-sample Mendelian randomization (MR) analysis, and 628,000 Europeans in a two-sample MR analysis. We identified two single nucleotide polymorphisms (SNPs) rs35691438 and rs671 that were significantly associated with serum copper levels (SCLs). The bidirectional two-sample MR analysis in the East Asian population showed that gamma-glutamyl transpeptidase levels have a causal effect on SCLs. SCLs have causal effects on six outcomes, namely risks of esophageal varix, glaucoma, sleep apnea syndrome, and systemic lupus erythematosus, white blood cell count, and usage of drugs affecting bone structure and mineralization. The two-sample MR analyses in the European population showed causal effects of erythrocyte copper levels on risks of carpal tunnel syndrome and compression fracture. Our results provide original insights into the causal relationship between blood metal levels and multiple human phenotypes. A genome-wide association study in a Chinese population identifies SNPs associated with serum copper levels. Mendelian randomization analysis reveals causal effects on multiple human phenotypes in East Asian and European populations.
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Avery CL, Howard AG, Ballou AF, Buchanan VL, Collins JM, Downie CG, Engel SM, Graff M, Highland HM, Lee MP, Lilly AG, Lu K, Rager JE, Staley BS, North KE, Gordon-Larsen P. Strengthening Causal Inference in Exposomics Research: Application of Genetic Data and Methods. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:55001. [PMID: 35533073 PMCID: PMC9084332 DOI: 10.1289/ehp9098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 05/11/2023]
Abstract
Advances in technologies to measure a broad set of exposures have led to a range of exposome research efforts. Yet, these efforts have insufficiently integrated methods that incorporate genetic data to strengthen causal inference, despite evidence that many exposome-associated phenotypes are heritable. Objective: We demonstrate how integration of methods and study designs that incorporate genetic data can strengthen causal inference in exposomics research by helping address six challenges: reverse causation and unmeasured confounding, comprehensive examination of phenotypic effects, low efficiency, replication, multilevel data integration, and characterization of tissue-specific effects. Examples are drawn from studies of biomarkers and health behaviors, exposure domains where the causal inference methods we describe are most often applied. Discussion: Technological, computational, and statistical advances in genotyping, imputation, and analysis, combined with broad data sharing and cross-study collaborations, offer multiple opportunities to strengthen causal inference in exposomics research. Full application of these opportunities will require an expanded understanding of genetic variants that predict exposome phenotypes as well as an appreciation that the utility of genetic variants for causal inference will vary by exposure and may depend on large sample sizes. However, several of these challenges can be addressed through international scientific collaborations that prioritize data sharing. Ultimately, we anticipate that efforts to better integrate methods that incorporate genetic data will extend the reach of exposomics research by helping address the challenges of comprehensively measuring the exposome and its health effects across studies, the life course, and in varied contexts and diverse populations. https://doi.org/10.1289/EHP9098.
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Affiliation(s)
- Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anna F Ballou
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victoria L Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason M Collins
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolina G Downie
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephanie M Engel
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Moa P Lee
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adam G Lilly
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Sociology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brooke S Staley
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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An Amish founder population reveals rare-population genetic determinants of the human lipidome. Commun Biol 2022; 5:334. [PMID: 35393526 PMCID: PMC8989972 DOI: 10.1038/s42003-022-03291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Identifying the genetic determinants of inter-individual variation in lipid species (lipidome) may provide deeper understanding and additional insight into the mechanistic effect of complex lipidomic pathways in CVD risk and progression beyond simple traditional lipids. Previous studies have been largely population based and thus only powered to discover associations with common genetic variants. Founder populations represent a powerful resource to accelerate discovery of previously unknown biology associated with rare population alleles that have risen to higher frequency due to genetic drift. We performed a genome-wide association scan of 355 lipid species in 650 individuals from the Amish founder population including 127 lipid species not previously tested. To the best of our knowledge, we report for the first time the lipid species associated with two rare-population but Amish-enriched lipid variants: APOB_rs5742904 and APOC3_rs76353203. We also identified novel associations for 3 rare-population Amish-enriched loci with several sphingolipids and with proposed potential functional/causal variant in each locus including GLTPD2_rs536055318, CERS5_rs771033566, and AKNA_rs531892793. We replicated 7 previously known common loci including novel associations with two sterols: androstenediol with UGT locus and estriol with SLC22A8/A24 locus. Our results show the double power of founder populations and detailed lipidome to discover novel trait-associated variants. A GWAS of 355 lipid species in the Old Order Amish founder population reveals associations between Amish-enriched loci and several sphingolipids.
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Pang Y, Kartsonaki C, Lv J, Millwood IY, Fairhurst-Hunter Z, Turnbull I, Bragg F, Hill MR, Yu C, Guo Y, Chen Y, Yang L, Clarke R, Walters RG, Wu M, Chen J, Li L, Chen Z, Holmes MV. Adiposity, metabolomic biomarkers, and risk of nonalcoholic fatty liver disease: a case-cohort study. Am J Clin Nutr 2022; 115:799-810. [PMID: 34902008 PMCID: PMC8895224 DOI: 10.1093/ajcn/nqab392] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/06/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Globally, the burden of obesity and associated nonalcoholic fatty liver disease (NAFLD) are rising, but little is known about the role that circulating metabolomic biomarkers play in mediating their association. OBJECTIVES We aimed to examine the observational and genetic associations of adiposity with metabolomic biomarkers and the observational associations of metabolomic biomarkers with incident NAFLD. METHODS A case-subcohort study within the prospective China Kadoorie Biobank included 176 NAFLD cases and 180 subcohort individuals and measured 1208 metabolites in stored baseline plasma using a Metabolon assay. In the subcohort the observational and genetic associations of BMI with biomarkers were assessed using linear regression, with adjustment for multiple testing. Cox regression was used to estimate adjusted HRs for NAFLD associated with biomarkers. RESULTS In observational analyses, BMI (kg/m2; mean: 23.9 in the subcohort) was associated with 199 metabolites at a 5% false discovery rate. The effects of genetically elevated BMI with specific metabolites were directionally consistent with the observational associations. Overall, 35 metabolites were associated with NAFLD risk, of which 15 were also associated with BMI, including glutamate (HR per 1-SD higher metabolite: 1.95; 95% CI: 1.48, 2.56), cysteine-glutathione disulfide (0.44; 0.31, 0.62), diaclyglycerol (C32:1) (1.71; 1.24, 2.35), behenoyl dihydrosphingomyelin (C40:0) (1.92; 1.42, 2.59), butyrylcarnitine (C4) (1.91; 1.38, 2.35), 2-hydroxybehenate (1.81; 1.34, 2.45), and 4-cholesten-3-one (1.79; 1.27, 2.54). The discriminatory performance of known risk factors was increased when 28 metabolites were also considered simultaneously in the model (weighted C-statistic: 0.84 to 0.90; P < 0.001). CONCLUSIONS Among relatively lean Chinese adults, a range of metabolomic biomarkers are associated with NAFLD risk and these biomarkers may lie on the pathway between adiposity and NAFLD.
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Affiliation(s)
- Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Christiana Kartsonaki
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response (PKU-PHEPR), Peking University, Beijing, China
| | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Zammy Fairhurst-Hunter
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Iain Turnbull
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Fiona Bragg
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Michael R Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response (PKU-PHEPR), Peking University, Beijing, China
| | - Yu Guo
- Chinese Academy of Medical Sciences, Beijing, China
| | - Yiping Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ling Yang
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Robert Clarke
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ming Wu
- Jiangsu Center for Disease Control and Prevention, Nanjing, China
| | - Junshi Chen
- National Center for Food Safety Risk Assessment, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response (PKU-PHEPR), Peking University, Beijing, China
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Michael V Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospital, Oxford, United Kingdom
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Di Narzo AF, Houten SM, Kosoy R, Huang R, Vaz FM, Hou R, Wei G, Wang WH, Comella PH, Dodatko T, Rogatsky E, Stojmirovic A, Brodmerkel C, Perrigoue J, Hart A, Curran M, Friedman JR, Zhu J, Agrawal M, Cho J, Ungaro R, Dubinsky M, Sands BE, Suárez-Fariñas M, Schadt EE, Colombel JF, Kasarskis A, Hao K, Argmann C. Integrative Analysis of the Inflammatory Bowel Disease Serum Metabolome Improves Our Understanding of Genetic Etiology and Points to Novel Putative Therapeutic Targets. Gastroenterology 2022; 162:828-843.e11. [PMID: 34780722 PMCID: PMC9214725 DOI: 10.1053/j.gastro.2021.11.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 11/01/2021] [Accepted: 11/07/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Polygenic and environmental factors are underlying causes of inflammatory bowel disease (IBD). We hypothesized that integration of the genetic loci controlling a metabolite's abundance, with known IBD genetic susceptibility loci, may help resolve metabolic drivers of IBD. METHODS We measured the levels of 1300 metabolites in the serum of 484 patients with ulcerative colitis (UC) and 464 patients with Crohn's disease (CD) and 365 controls. Differential metabolite abundance was determined for disease status, subtype, clinical and endoscopic disease activity, as well as IBD phenotype including disease behavior, location, and extent. To inform on the genetic basis underlying metabolic diversity, we integrated metabolite and genomic data. Genetic colocalization and Mendelian randomization analyses were performed using known IBD risk loci to explore whether any metabolite was causally associated with IBD. RESULTS We found 173 genetically controlled metabolites (metabolite quantitative trait loci, 9 novel) within 63 non-overlapping loci (7 novel). Furthermore, several metabolites significantly associated with IBD disease status and activity as defined using clinical and endoscopic indexes. This constitutes a resource for biomarker discovery and IBD biology insights. Using this resource, we show that a novel metabolite quantitative trait locus for serum butyrate levels containing ACADS was not supported as causal for IBD; replicate the association of serum omega-6 containing lipids with the fatty acid desaturase 1/2 locus and identify these metabolites as causal for CD through Mendelian randomization; and validate a novel association of serum plasmalogen and TMEM229B, which was predicted as causal for CD. CONCLUSIONS An exploratory analysis combining genetics and unbiased serum metabolome surveys can reveal novel biomarkers of disease activity and potential mediators of pathology in IBD.
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Affiliation(s)
- Antonio F. Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Corresponding Author: Carmen Argmann,
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Ruiqi Huang
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frédéric M. Vaz
- Department of Clinical Chemistry, Amsterdam Gastroenterology & Metabolism, Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruixue Hou
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Wen-hui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Eduard Rogatsky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | | | | | | | - Amy Hart
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | - Mark Curran
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | | | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Manasi Agrawal
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, New York, New York.
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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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Jaskiw GE, Xu D, Obrenovich ME, Donskey CJ. Small phenolic and indolic gut-dependent molecules in the primate central nervous system: levels vs. bioactivity. Metabolomics 2022; 18:8. [PMID: 34989922 DOI: 10.1007/s11306-021-01866-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/12/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION A rapidly growing body of data documents associations between disease of the brain and small molecules generated by gut-microbiota (GMB). While such metabolites can affect brain function through a variety of mechanisms, the most direct action would be on the central nervous system (CNS) itself. OBJECTIVE Identify indolic and phenolic GMB-dependent small molecules that reach bioactive concentrations in primate CNS. METHODS We conducted a PubMed search for metabolomic studies of the primate CNS [brain tissue or cerebrospinal fluid (CSF)] and then selected for phenolic or indolic metabolites that (i) had been quantified, (ii) were GMB-dependent. For each chemical we then conducted a search for studies of bioactivity conducted in vitro in human cells of any kind or in CNS cells from the mouse or rat. RESULTS 36 metabolites of interests were identified in primate CNS through targeted metabolomics. Quantification was available for 31/36 and in vitro bioactivity for 23/36. The reported CNS range for 8 metabolites 2-(3-hydroxyphenyl)acetic acid, 2-(4-hydroxyphenyl)acetic acid, 3-(3-hydroxyphenyl)propanoic acid, (E)-3-(3,4-dihydroxyphenyl)prop-2-enoic acid [caffeic acid], 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, 2-acetamido-3-(1H-indol-3-yl)propanoic acid [N-acetyltryptophan], 1H-indol-3-yl hydrogen sulfate [indoxyl-3-sulfate] overlapped with a bioactive concentration. However, the number and quality of relevant studies of CNS neurochemistry as well as of bioactivity were highly limited. Structural isomers, multiple metabolites and potential confounders were inadequately considered. CONCLUSION The potential direct bioactivity of GMB-derived indolic and phenolic molecules on primate CNS remains largely unknown. The field requires additional strategies to identify and prioritize screening of the most promising small molecules that enter the CNS.
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Affiliation(s)
- George E Jaskiw
- Psychiatry Service 116(A), Veterans Affairs Northeast Ohio Healthcare System (VANEOHS), 10701 East Blvd., Cleveland, OH, 44106, USA.
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Dongyan Xu
- Psychiatry Service 116(A), Veterans Affairs Northeast Ohio Healthcare System (VANEOHS), 10701 East Blvd., Cleveland, OH, 44106, USA
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mark E Obrenovich
- Pathology and Laboratory Medicine Service, VANEOHS, Cleveland, OH, USA
- Research Service, VANEOHS, Cleveland, OH, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis J Donskey
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Geriatric Research, Education and Clinical Center (GRECC), VANEOHS, Cleveland, OH, USA
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Huang SY, Yang YX, Zhang YR, Kuo K, Li HQ, Shen XN, Chen SD, Chen KL, Dong Q, Tan L, Yu JT. Investigating Causal Relations Between Circulating Metabolites and Alzheimer's Disease: A Mendelian Randomization Study. J Alzheimers Dis 2022; 87:463-477. [PMID: 35275550 DOI: 10.3233/jad-220050] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Metabolomics is a promising approach that can be used to understand pathophysiological pathways of Alzheimer's disease (AD). However, the causal relationships between metabolism and AD are poorly understood. OBJECTIVE We aimed to investigate the causal association between circulating metabolites and risk of AD through two-sample Mendelian randomization (MR) approach. METHODS Genetic associations with 123 circulating metabolic traits were utilized as exposures. Summary statistics data from International Genomics of Alzheimer's Project was used in primary analysis, including 21,982 AD cases and 41,944 controls. Validation was performed using family history of AD data from UK Biobank (27,696 cases of maternal AD, 14,338 cases of paternal AD, and 272,244 controls). We utilized inverse-variance weighted method as primary method. RESULTS We found significantly increased risks of developing AD per standard deviation increase in the levels of circulating ApoB (odd ratio[OR] = 3.18; 95% confidence interval[CI]: 1.52-6.66, p = 0.0022), glycoprotein acetyls (OR = 1.21; 95% CI: 1.05-1.39, p = 0.0093), total cholesterol (OR = 2.73; 95% CI: 1.41-5.30, p = 0.0030), and low-density lipoprotein (LDL) cholesterol (OR = 2.34; 95% CI: 1.53-3.57, p = 0.0001). Whereas glutamine (OR = 0.81; 95% CI: 0.71-0.92, p = 0.0011) were significantly associated with lower risk of AD. We also detected causal effects of several different composition of LDL fractions on increased AD risk, which has been verified in validation. However, we found no association between circulating high-density lipoprotein cholesterol and AD. CONCLUSION Our findings suggest causal effects of circulating glycoprotein acetyls, ApoB, LDL cholesterol, and serum total cholesterol on higher risk of AD, whereas glutamine showed the protective effect.
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Affiliation(s)
- Shu-Yi Huang
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Yu-Xiang Yang
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Ya-Ru Zhang
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Kevin Kuo
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Hong-Qi Li
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Xue-Ning Shen
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Shi-Dong Chen
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Ke-Liang Chen
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, China
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43
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van der Spek A, Karamujić-Čomić H, Pool R, Bot M, Beekman M, Garmaeva S, Arp PP, Henkelman S, Liu J, Alves AC, Willemsen G, van Grootheest G, Aubert G, Ikram MA, Jarvelin MR, Lansdorp P, Uitterlinden AG, Zhernakova A, Slagboom PE, Penninx BWJH, Boomsma DI, Amin N, van Duijn CM. Fat metabolism is associated with telomere length in six population-based studies. Hum Mol Genet 2021; 31:1159-1170. [PMID: 34875050 DOI: 10.1093/hmg/ddab281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/13/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
Telomeres are repetitive DNA sequences located at the end of chromosomes, which are associated to biological aging, cardiovascular disease, cancer, and mortality. Lipid and fatty acid metabolism have been associated with telomere shortening. We have conducted an in-depth study investigating the association of metabolic biomarkers with telomere length (LTL). We performed an association analysis of 226 metabolic biomarkers with LTL using data from 11 775 individuals from six independent population-based cohorts (BBMRI-NL consortium). Metabolic biomarkers include lipoprotein lipids and subclasses, fatty acids, amino acids, glycolysis measures and ketone bodies. LTL was measured by quantitative polymerase chain reaction or FlowFISH. Linear regression analysis was performed adjusting for age, sex, lipid-lowering medication and cohort-specific covariates (model 1) and additionally for body mass index (BMI) and smoking (model 2), followed by inverse variance-weighted meta-analyses (significance threshold pmeta = 6.5x10-4). We identified four metabolic biomarkers positively associated with LTL, including two cholesterol to lipid ratios in small VLDL (S-VLDL-C % and S-VLDL-ce %) and two omega-6 fatty acid ratios (FAw6/FA and LA/FA). After additionally adjusting for BMI and smoking, these metabolic biomarkers remained associated with LTL with similar effect estimates. In addition, cholesterol esters in very small VLDL (XS-VLDL-ce) became significantly associated with LTL (p = 3.6x10-4). We replicated the association of FAw6/FA with LTL in an independent dataset of 7845 individuals (p = 1.9x10-4). To conclude, we identified multiple metabolic biomarkers involved in lipid and fatty acid metabolism that may be involved in LTL biology. Longitudinal studies are needed to exclude reversed causation.
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Affiliation(s)
- Ashley van der Spek
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,SkylineDx B.V., Rotterdam, The Netherlands
| | - Hata Karamujić-Čomić
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit University Amsterdam, Amsterdam, The Netherlands.,Amsterdam Public Health research institute, Amsterdam University Medical Centers, The Netherlands.,BBMRI-NL: Infrastructure for the Application of Metabolomics Technology in Epidemiology (RP4), The Netherlands
| | - Mariska Bot
- Department of Psychiatry and GGZ in Geest, Amsterdam Public Health research institute and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pascal P Arp
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Sandra Henkelman
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jun Liu
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom.,School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit University Amsterdam, Amsterdam, The Netherlands.,Amsterdam Public Health research institute, Amsterdam University Medical Centers, The Netherlands
| | - Gerard van Grootheest
- Department of Psychiatry and GGZ in Geest, Amsterdam Public Health research institute and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - Geraldine Aubert
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, V5Z 1L3 British Columbia, Canada
| | | | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom.,Center for Life Course Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Peter Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, V5Z 1L3 British Columbia, Canada.,Departments of Medical Genetics and Hematology, University of British Columbia, Vancouver, V6T 1Z4 British Columbia, Canada
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry and GGZ in Geest, Amsterdam Public Health research institute and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit University Amsterdam, Amsterdam, The Netherlands.,Amsterdam Public Health research institute, Amsterdam University Medical Centers, The Netherlands.,BBMRI-NL: Infrastructure for the Application of Metabolomics Technology in Epidemiology (RP4), The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, UK
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44
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Genetic overlap and causality between blood metabolites and migraine. Am J Hum Genet 2021; 108:2086-2098. [PMID: 34644541 DOI: 10.1016/j.ajhg.2021.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
The availability of genome-wide association studies (GWASs) for human blood metabolome provides an excellent opportunity for studying metabolism in a heritable disease such as migraine. Utilizing GWAS summary statistics, we conduct comprehensive pairwise genetic analyses to estimate polygenic genetic overlap and causality between 316 unique blood metabolite levels and migraine risk. We find significant genome-wide genetic overlap between migraine and 44 metabolites, mostly lipid and organic acid metabolic traits (FDR < 0.05). We also identify 36 metabolites, mostly related to lipoproteins, that have shared genetic influences with migraine at eight independent genomic loci (posterior probability > 0.9) across chromosomes 3, 5, 6, 9, and 16. The observed relationships between genetic factors influencing blood metabolite levels and genetic risk for migraine suggest an alteration of metabolite levels in individuals with migraine. Our analyses suggest higher levels of fatty acids, except docosahexaenoic acid (DHA), a very long-chain omega-3, in individuals with migraine. Consistently, we found a causally protective role for a longer length of fatty acids against migraine. We also identified a causal effect for a higher level of a lysophosphatidylethanolamine, LPE(20:4), on migraine, thus introducing LPE(20:4) as a potential therapeutic target for migraine.
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Al Rashid K, Goulding N, Taylor A, Lumsden MA, Lawlor DA, Nelson SM. Spousal associations of serum metabolomic profiles by nuclear magnetic resonance spectroscopy. Sci Rep 2021; 11:21587. [PMID: 34732718 PMCID: PMC8566506 DOI: 10.1038/s41598-021-00531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Phenotype-based assortative mating is well established in humans, with the potential for further convergence through a shared environment. To assess the correlation within infertile couples of physical, social, and behavioural characteristics and 155 circulating metabolic measures. Cross sectional study at a tertiary medical center of 326 couples undertaking IVF. Serum lipids, lipoprotein subclasses, and low-molecular weight metabolites as quantified by NMR spectroscopy (155 metabolic measures). Multivariable and quantile regression correlations within couples of metabolite profiles. Couples exhibited statistical correlations of varying strength for most physical, social, and behavioural characteristics including age, height, alcohol consumption, education, smoking status, physical activity, family history and ethnicity, with correlation coefficients ranging from 0.22 to 0.73. There was no evidence of within couple associations for BMI and weight, where the correlation coefficients were - 0.03 (95% CI - 0.14, 0.08) and 0.01 (95% CI - 0.10, 0.12), respectively. Within spousal associations of the metabolite measurements were all positive but with weak to modest magnitudes, with the median correlation coefficient across all 155 measures being 0.12 (range 0.01-0.37 and interquartile range 0.10-0.18). With just four having associations stronger than 0.3: docosahexaenoic acid (0.37, 95% CI 0.22, 0.52), omega-3 fatty acids (0.32, 95% CI 0.20, 0.43) histidine (0.32, 95% CI 0.23, 0.41) and pyruvate (0.32, 95% CI 0.22, 0.43). Infertile couples exhibit spousal similarities for a range of demographic and serum metabolite measures, supporting initial assortative mating, with diet-derived metabolites suggesting possible subsequent convergence of their individual metabolic profile.
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Affiliation(s)
- Karema Al Rashid
- School of Medicine, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Neil Goulding
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 2BN, UK
- Bristol Medical School, Population Health Science, Bristol, UK
| | - Amy Taylor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 2BN, UK
- Bristol Medical School, Population Health Science, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Mary Ann Lumsden
- School of Medicine, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 2BN, UK
- Bristol Medical School, Population Health Science, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Scott M Nelson
- School of Medicine, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK.
- NIHR Bristol Biomedical Research Centre, Bristol, UK.
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Heritability and genetic correlations of plasma metabolites of pigs with production, resilience and carcass traits under natural polymicrobial disease challenge. Sci Rep 2021; 11:20628. [PMID: 34667249 PMCID: PMC8526711 DOI: 10.1038/s41598-021-99778-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Metabolites in plasma of healthy nursery pigs were quantified using nuclear magnetic resonance. Heritabilities of metabolite concentration were estimated along with their phenotypic and genetic correlations with performance, resilience, and carcass traits in growing pigs exposed to a natural polymicrobial disease challenge. Variance components were estimated by GBLUP. Heritability estimates were low to moderate (0.11 ± 0.08 to 0.19 ± 0.08) for 14 metabolites, moderate to high (0.22 ± 0.09 to 0.39 ± 0.08) for 17 metabolites, and highest for l-glutamic acid (0.41 ± 0.09) and hypoxanthine (0.42 ± 0.08). Phenotypic correlation estimates of plasma metabolites with performance and carcass traits were generally very low. Significant genetic correlation estimates with performance and carcass traits were found for several measures of growth and feed intake. Interestingly the plasma concentration of oxoglutarate was genetically negatively correlated with treatments received across the challenge nursery and finisher (− 0.49 ± 0.28; P < 0.05) and creatinine was positively correlated with mortality in the challenge nursery (0.85 ± 0.76; P < 0.05). These results suggest that some plasma metabolite phenotypes collected from healthy nursery pigs are moderately heritable and genetic correlations with measures of performance and resilience after disease challenge suggest they may be potential genetic indicators of disease resilience.
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Fu J, Zhang Y, Liu J, Lian X, Tang J, Zhu F. Pharmacometabonomics: data processing and statistical analysis. Brief Bioinform 2021; 22:6236068. [PMID: 33866355 DOI: 10.1093/bib/bbab138] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Individual variations in drug efficacy, side effects and adverse drug reactions are still challenging that cannot be ignored in drug research and development. The aim of pharmacometabonomics is to better understand the pharmacokinetic properties of drugs and monitor the drug effects on specific metabolic pathways. Here, we systematically reviewed the recent technological advances in pharmacometabonomics for better understanding the pathophysiological mechanisms of diseases as well as the metabolic effects of drugs on bodies. First, the advantages and disadvantages of all mainstream analytical techniques were compared. Second, many data processing strategies including filtering, missing value imputation, quality control-based correction, transformation, normalization together with the methods implemented in each step were discussed. Third, various feature selection and feature extraction algorithms commonly applied in pharmacometabonomics were described. Finally, the databases that facilitate current pharmacometabonomics were collected and discussed. All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jin Liu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Xichen Lian
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jing Tang
- Department of Bioinformatics in Chongqing Medical University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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Chen L, Abel HJ, Das I, Larson DE, Ganel L, Kanchi KL, Regier AA, Young EP, Kang CJ, Scott AJ, Chiang C, Wang X, Lu S, Christ R, Service SK, Chiang CWK, Havulinna AS, Kuusisto J, Boehnke M, Laakso M, Palotie A, Ripatti S, Freimer NB, Locke AE, Stitziel NO, Hall IM. Association of structural variation with cardiometabolic traits in Finns. Am J Hum Genet 2021; 108:583-596. [PMID: 33798444 PMCID: PMC8059371 DOI: 10.1016/j.ajhg.2021.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/03/2021] [Indexed: 02/08/2023] Open
Abstract
The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.
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Affiliation(s)
- Lei Chen
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Indraniel Das
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liron Ganel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Krishna L Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica P Young
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Alexandra J Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Colby Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xinxin Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ryan Christ
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Susan K Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Finnish Institute for Health and Welfare (THL), Helsinki 00271, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland; Department of Medicine, Kuopio University Hospital, Kuopio 70210, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland; Department of Medicine, Kuopio University Hospital, Kuopio 70210, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Adam E Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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Rahman ML, Doyon M, Arguin M, Perron P, Bouchard L, Hivert MF. A prospective study of maternal adiposity and glycemic traits across pregnancy and mid-childhood metabolomic profiles. Int J Obes (Lond) 2021; 45:860-869. [PMID: 33504931 DOI: 10.1038/s41366-021-00750-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/14/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND Fetal exposure to maternal excess adiposity and hyperglycemia is risk factors for childhood adverse metabolic outcomes. Using data from a prospective pre-birth cohort, we aimed to further understand the prenatal determinants of fetal metabolic programming based on analyses of maternal adiposity and glycemic traits across pregnancy with childhood metabolomic profiles. METHODS This study included 330 mother-child pairs from the Gen3G cohort with information on maternal adiposity and glycemic markers at 5-16 (visit 1) and 24-30 (visit 2) weeks of pregnancy. At mid-childhood (4.8-7.2 years old), we collected fasting plasma and measured 1116 metabolites using an untargeted approach. We constructed networks of interconnected metabolites using a weighted-correlation network analysis algorithm. We estimated Spearman's partial correlation coefficients of maternal adiposity and glycemic traits across pregnancy with metabolite networks and individual metabolites, adjusting for maternal age, gravidity, race/ethnicity, history of smoking, and child's sex and age at blood collection for metabolite measurement. RESULTS We identified a network of 16 metabolites, primarily glycero-3-phosphoethanolamines (GPE) at mid-childhood that showed consistent negative correlations with maternal body mass index, waist circumference, and body-fat percentage at visits 1 and 2 (ρadjusted = -0.14 to -0.21) and post-challenge glucose levels at visit 2 (ρadjusted = -0.10 to -0.13), while positive correlations with Matsuda index (ρadjusted = 0.13). Within this identified network, 1-palmitoyl-2-decosahexaenoyl-GPE and 1-stearoyl-2-decosahexaenoyl-GPE appeared to be driving the associations. In addition, a network of 89 metabolites, primarily phosphatidylcholines, plasmalogens, sphingomyelins, and ceramides showed consistent negative correlations with insulin at visit 1 and post-challenge glucose at visit 2, while positive correlation with adiponectin at visit 2. CONCLUSIONS Prenatal exposure to maternal higher adiposity and hyperglycemic traits and lower insulin sensitivity markers were associated with a unique metabolomic pattern characterized by low serum phospho- and sphingolipids in mid-childhood.
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Affiliation(s)
- Mohammad L Rahman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Myriam Doyon
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Melina Arguin
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada.,Faculty of Medicine and Life Sciences, Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada.,Faculty of Medicine and Life Sciences, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada.,Department of Medical Biology, CIUSSS du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA. .,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada. .,Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA.
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50
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Genomic-Metabolomic Associations Support the Role of LIPC and Glycerophospholipids in Age-Related Macular Degeneration. OPHTHALMOLOGY SCIENCE 2021; 1. [PMID: 34382031 PMCID: PMC8353724 DOI: 10.1016/j.xops.2021.100017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Purpose Large-scale genome-wide association studies (GWAS) have reported important single nucleotide polymorphisms (SNPs) with significant associations with age-related macular degeneration (AMD). However, their role in disease development remains elusive. This study aimed to assess SNP–metabolite associations (i.e., metabolite quantitative trait loci [met-QTL]) and to provide insights into the biological mechanisms of AMD risk SNPs. Design Cross-sectional multicenter study (Boston, Massachusetts, and Coimbra, Portugal). Participants Patients with AMD (n = 388) and control participants (n = 98) without any vitreoretinal disease (> 50 years). Methods Age-related macular degeneration grading was performed using color fundus photographs according to the Age-Related Eye Disease Study classification scheme. Fasting blood samples were collected and evaluated with mass spectrometry for metabolomic profiling and Illumina OmniExpress for SNPs profiling. Analyses of met-QTL of endogenous metabolites were conducted using linear regression models adjusted for age, gender, smoking, 10 metabolite principal components (PCs), and 10 SNP PCs. Additionally, we analyzed the cumulative effect of AMD risk SNPs on plasma metabolites by generating genetic risk scores and assessing their associations with metabolites using linear regression models, accounting for the same covariates. Modeling was performed first for each cohort, and then combined by meta-analysis. Multiple comparisons were accounted for using the false discovery rate (FDR). Main Outcome Measures Plasma metabolite levels associated with AMD risk SNPs. Results After quality control, data for 544 plasma metabolites were included. Meta-analysis of data from all individuals (AMD patients and control participants) identified 28 significant met-QTL (β = 0.016–0.083; FDR q-value < 1.14 × 10–2), which corresponded to 5 metabolites and 2 genes: ASPM and LIPC. Polymorphisms in the LIPC gene were associated with phosphatidylethanolamine metabolites, which are glycerophospholipids, and polymorphisms in the ASPM gene with branched-chain amino acids. Similar results were observed when considering only patients with AMD. Genetic risk score–metabolite associations further supported a global impact of AMD risk SNPs on the plasma metabolome. Conclusions This study demonstrated that genomic–metabolomic associations can provide insights into the biological relevance of AMD risk SNPs. In particular, our results support that the LIPC gene and the glycerophospholipid metabolic pathway may play an important role in AMD, thus offering new potential therapeutic targets for this disease.
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