1
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Zheng K, Qian Y, Wang H, Song D, You H, Hou B, Han F, Zhu Y, Feng F, Lam SM, Shui G, Li X. Combinatorial lipidomics and proteomics underscore erythrocyte lipid membrane aberrations in the development of adverse cardio-cerebrovascular complications in maintenance hemodialysis patients. Redox Biol 2024; 76:103295. [PMID: 39159596 PMCID: PMC11378344 DOI: 10.1016/j.redox.2024.103295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/21/2024] [Accepted: 07/31/2024] [Indexed: 08/21/2024] Open
Abstract
Age-associated deterioration of physiological functions occur at heterogeneous rates across individual organs. A granular evaluation of systemic metabolic mediators of aging in a healthy human cohort (n = 225) identified prominent increases in circulating uremic toxins that were recapitulated in mice, on which we further characterized the aging phenome across five peripheral organs. Our multi-omics analyses connected systemic aging profiles primarily to kidney metabolism, uncovering a metabolic association between localized glucosylceramide (GluCer) accretion and renal functional decline. Elevated GluCers were also associated with higher risk of deaths in an independent cohort of aged individuals (n = 271). We report GluCer-mTOR signaling commencing at late middle-age that disrupts mitophagy and undermines mitochondrial respiration in kidney. Conserved between human and mice, GluCer-mediated renal dysfunction is female-biased and modulated by intracellular purines. Our work provides molecular basis for the sexually disparate effects of mTOR inhibition on mammalian lifespan, possibly ascribed to the evolutionary cost of female reproduction.
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Affiliation(s)
- Ke Zheng
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yujun Qian
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China; Department of Nephrology, Jiangsu Province Hospital/The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haiyun Wang
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dan Song
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Hui You
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Hou
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Han
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yicheng Zhu
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Feng
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Xuemei Li
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.
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Lee AM, Xu Y, Hu J, Xiao R, Hooper SR, Hartung EA, Coresh J, Rhee EP, Vasan RS, Kimmel PL, Warady BA, Furth SL, Denburg MR. Longitudinal Plasma Metabolome Patterns and Relation to Kidney Function and Proteinuria in Pediatric CKD. Clin J Am Soc Nephrol 2024; 19:837-850. [PMID: 38709558 PMCID: PMC11254025 DOI: 10.2215/cjn.0000000000000463] [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: 12/20/2023] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
Key Points Longitudinal untargeted metabolomics. Children with CKD have a circulating metabolome that changes over time. Background Understanding plasma metabolome patterns in relation to changing kidney function in pediatric CKD is important for continued research for identifying novel biomarkers, characterizing biochemical pathophysiology, and developing targeted interventions. There are a limited number of studies of longitudinal metabolomics and virtually none in pediatric CKD. Methods The CKD in Children study is a multi-institutional, prospective cohort that enrolled children aged 6 months to 16 years with eGFR 30–90 ml/min per 1.73 m2. Untargeted metabolomics profiling was performed on plasma samples from the baseline, 2-, and 4-year study visits. There were technologic updates in the metabolomic profiling platform used between the baseline and follow-up assays. Statistical approaches were adopted to avoid direct comparison of baseline and follow-up measurements. To identify metabolite associations with eGFR or urine protein-creatinine ratio (UPCR) among all three time points, we applied linear mixed-effects (LME) models. To identify metabolites associated with time, we applied LME models to the 2- and 4-year follow-up data. We applied linear regression analysis to examine associations between change in metabolite level over time (∆level) and change in eGFR (∆eGFR) and UPCR (∆UPCR). We reported significance on the basis of both the false discovery rate (FDR) <0.05 and P < 0.05. Results There were 1156 person-visits (N : baseline=626, 2-year=254, 4-year=276) included. There were 622 metabolites with standardized measurements at all three time points. In LME modeling, 406 and 343 metabolites associated with eGFR and UPCR at FDR <0.05, respectively. Among 530 follow-up person-visits, 158 metabolites showed differences over time at FDR <0.05. For participants with complete data at both follow-up visits (n =123), we report 35 metabolites with ∆level–∆eGFR associations significant at FDR <0.05. There were no metabolites with significant ∆level–∆UPCR associations at FDR <0.05. We report 16 metabolites with ∆level–∆UPCR associations at P < 0.05 and associations with UPCR in LME modeling at FDR <0.05. Conclusions We characterized longitudinal plasma metabolomic patterns associated with eGFR and UPCR in a large pediatric CKD population. Many of these metabolite signals have been associated with CKD progression, etiology, and proteinuria in previous CKD Biomarkers Consortium studies. There were also novel metabolite associations with eGFR and proteinuria detected.
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Affiliation(s)
- Arthur M. Lee
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yunwen Xu
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Jian Hu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Rui Xiao
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R. Hooper
- Department of Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina
| | - Erum A. Hartung
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- NYU Grossman School of Medicine, New York, New York
| | - Eugene P. Rhee
- Division of Nephrology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Boston University School of Medicine, Boston, Massachusetts
- Boston University School of Public Health, Boston, Massachusetts
| | - Paul L. Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Bradley A. Warady
- Division of Nephrology, Children’s Mercy Kansas City, Kansas City, Missouri
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Susan L. Furth
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
- Department of Pediatrics and Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michelle R. Denburg
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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3
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Chrysopoulou M, Rinschen MM. Metabolic Rewiring and Communication: An Integrative View of Kidney Proximal Tubule Function. Annu Rev Physiol 2024; 86:405-427. [PMID: 38012048 DOI: 10.1146/annurev-physiol-042222-024724] [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] [Indexed: 11/29/2023]
Abstract
The kidney proximal tubule is a key organ for human metabolism. The kidney responds to stress with altered metabolite transformation and perturbed metabolic pathways, an ultimate cause for kidney disease. Here, we review the proximal tubule's metabolic function through an integrative view of transport, metabolism, and function, and embed it in the context of metabolome-wide data-driven research. Function (filtration, transport, secretion, and reabsorption), metabolite transformation, and metabolite signaling determine kidney metabolic rewiring in disease. Energy metabolism and substrates for key metabolic pathways are orchestrated by metabolite sensors. Given the importance of renal function for the inner milieu, we also review metabolic communication routes with other organs. Exciting research opportunities exist to understand metabolic perturbation of kidney and proximal tubule function, for example, in hypertension-associated kidney disease. We argue that, based on the integrative view outlined here, kidney diseases without genetic cause should be approached scientifically as metabolic diseases.
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Affiliation(s)
| | - Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark;
- III. Department of Medicine and Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
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4
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Louck LE, Cara KC, Klatt K, Wallace TC, Chung M. The Relationship of Circulating Choline and Choline-Related Metabolite Levels with Health Outcomes: A Scoping Review of Genome-Wide Association Studies and Mendelian Randomization Studies. Adv Nutr 2024; 15:100164. [PMID: 38128611 PMCID: PMC10819410 DOI: 10.1016/j.advnut.2023.100164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
Choline is essential for proper liver, muscle, brain, lipid metabolism, cellular membrane composition, and repair. Understanding genetic determinants of circulating choline metabolites can help identify new determinants of choline metabolism, requirements, and their link to disease endpoints. We conducted a scoping review to identify studies assessing the association of genetic polymorphisms on circulating choline and choline-related metabolite concentrations and subsequent associations with health outcomes. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement scoping review extension. Literature was searched to September 28, 2022, in 4 databases: Embase, MEDLINE, Web of Science, and the Biological Science Index. Studies of any duration in humans were considered. Any genome-wide association study (GWAS) investigating genetic variant associations with circulating choline and/or choline-related metabolites and any Mendelian randomization (MR) study investigating the association of genetically predicted circulating choline and/or choline-related metabolites with any health outcome were considered. Qualitative evidence is presented in summary tables. From 1248 total reviewed articles, 53 were included (GWAS = 27; MR = 26). Forty-two circulating choline-related metabolites were tested in association with genetic variants in GWAS studies, primarily trimethylamine N-oxide, betaine, sphingomyelins, lysophosphatidylcholines, and phosphatidylcholines. MR studies investigated associations between 52 total unique choline metabolites and 66 unique health outcomes. Of these, 47 significant associations were reported between 16 metabolites (primarily choline, lysophosphatidylcholines, phosphatidylcholines, betaine, and sphingomyelins) and 27 health outcomes including cancer, cardiovascular, metabolic, bone, and brain-related outcomes. Some articles reported significant associations between multiple choline types and the same health outcome. Genetically predicted circulating choline and choline-related metabolite concentrations are associated with a wide variety of health outcomes. Further research is needed to assess how genetic variability influences choline metabolism and whether individuals with lower genetically predicted circulating choline and choline-related metabolite concentrations would benefit from a dietary intervention or supplementation.
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Affiliation(s)
- Lauren E Louck
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Kelly C Cara
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Kevin Klatt
- Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States
| | - Taylor C Wallace
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States; Think Health Group, Inc, Washington, DC, United States
| | - Mei Chung
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States.
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Szrok-Jurga S, Czumaj A, Turyn J, Hebanowska A, Swierczynski J, Sledzinski T, Stelmanska E. The Physiological and Pathological Role of Acyl-CoA Oxidation. Int J Mol Sci 2023; 24:14857. [PMID: 37834305 PMCID: PMC10573383 DOI: 10.3390/ijms241914857] [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: 08/25/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Fatty acid metabolism, including β-oxidation (βOX), plays an important role in human physiology and pathology. βOX is an essential process in the energy metabolism of most human cells. Moreover, βOX is also the source of acetyl-CoA, the substrate for (a) ketone bodies synthesis, (b) cholesterol synthesis, (c) phase II detoxication, (d) protein acetylation, and (d) the synthesis of many other compounds, including N-acetylglutamate-an important regulator of urea synthesis. This review describes the current knowledge on the importance of the mitochondrial and peroxisomal βOX in various organs, including the liver, heart, kidney, lung, gastrointestinal tract, peripheral white blood cells, and other cells. In addition, the diseases associated with a disturbance of fatty acid oxidation (FAO) in the liver, heart, kidney, lung, alimentary tract, and other organs or cells are presented. Special attention was paid to abnormalities of FAO in cancer cells and the diseases caused by mutations in gene-encoding enzymes involved in FAO. Finally, issues related to α- and ω- fatty acid oxidation are discussed.
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Affiliation(s)
- Sylwia Szrok-Jurga
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Jacek Turyn
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Areta Hebanowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Julian Swierczynski
- Institue of Nursing and Medical Rescue, State University of Applied Sciences in Koszalin, 75-582 Koszalin, Poland;
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Ewa Stelmanska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
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Riguene E, Theodoridou M, Barrak L, Elrayess MA, Nomikos M. The Relationship between Changes in MYBPC3 Single-Nucleotide Polymorphism-Associated Metabolites and Elite Athletes' Adaptive Cardiac Function. J Cardiovasc Dev Dis 2023; 10:400. [PMID: 37754829 PMCID: PMC10531821 DOI: 10.3390/jcdd10090400] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/16/2023] [Indexed: 09/28/2023] Open
Abstract
Athletic performance is a multifactorial trait influenced by a complex interaction of environmental and genetic factors. Over the last decades, understanding and improving elite athletes' endurance and performance has become a real challenge for scientists. Significant tools include but are not limited to the development of molecular methods for talent identification, personalized exercise training, dietary requirements, prevention of exercise-related diseases, as well as the recognition of the structure and function of the genome in elite athletes. Investigating the genetic markers and phenotypes has become critical for elite endurance surveillance. The identification of genetic variants contributing to a predisposition for excellence in certain types of athletic activities has been difficult despite the relatively high genetic inheritance of athlete status. Metabolomics can potentially represent a useful approach for gaining a thorough understanding of various physiological states and for clarifying disorders caused by strength-endurance physical exercise. Based on a previous GWAS study, this manuscript aims to discuss the association of specific single-nucleotide polymorphisms (SNPs) located in the MYBPC3 gene encoding for cardiac MyBP-C protein with endurance athlete status. MYBPC3 is linked to elite athlete heart remodeling during or after exercise, but it could also be linked to the phenotype of cardiac hypertrophy (HCM). To make the distinction between both phenotypes, specific metabolites that are influenced by variants in the MYBPC3 gene are analyzed in relation to elite athletic performance and HCM. These include theophylline, ursodeoxycholate, quinate, and decanoyl-carnitine. According to the analysis of effect size, theophylline, quinate, and decanoyl carnitine increase with endurance while decreasing with cardiovascular disease, whereas ursodeoxycholate increases with cardiovascular disease. In conclusion, and based on our metabolomics data, the specific effects on athletic performance for each MYBPC3 SNP-associated metabolite are discussed.
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Affiliation(s)
- Emna Riguene
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
| | - Maria Theodoridou
- Biomedical Research Center (BRC), Qatar University, Doha P.O. Box 2713, Qatar;
| | - Laila Barrak
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
| | - Mohamed A. Elrayess
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
- Biomedical Research Center (BRC), Qatar University, Doha P.O. Box 2713, Qatar;
| | - Michail Nomikos
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (E.R.); (L.B.); (M.A.E.)
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Rhee EP, Surapaneni AL, Schlosser P, Alotaibi M, Yang YN, Coresh J, Jain M, Cheng S, Yu B, Grams ME. A genome-wide association study identifies 41 loci associated with eicosanoid levels. Commun Biol 2023; 6:792. [PMID: 37524825 PMCID: PMC10390489 DOI: 10.1038/s42003-023-05159-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023] Open
Abstract
Eicosanoids are biologically active derivatives of polyunsaturated fatty acids with broad relevance to health and disease. We report a genome-wide association study in 8406 participants of the Atherosclerosis Risk in Communities Study, identifying 41 loci associated with 92 eicosanoids and related metabolites. These findings highlight loci required for eicosanoid biosynthesis, including FADS1-3, ELOVL2, and numerous CYP450 loci. In addition, significant associations implicate a range of non-oxidative lipid metabolic processes in eicosanoid regulation, including at PKD2L1/SCD and several loci involved in fatty acyl-CoA metabolism. Further, our findings highlight select clearance mechanisms, for example, through the hepatic transporter encoded by SLCO1B1. Finally, we identify eicosanoids associated with aspirin and non-steroidal anti-inflammatory drug use and demonstrate the substantial impact of genetic variants even for medication-associated eicosanoids. These findings shed light on both known and unknown aspects of eicosanoid metabolism and motivate interest in several gene-eicosanoid associations as potential functional participants in human disease.
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Affiliation(s)
- Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA.
| | - Aditya L Surapaneni
- Division of Precision Medicine, New York University School of Medicine, New York, NY, USA
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mona Alotaibi
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yueh-Ning Yang
- Department of Epidemiology, Human Genetics & Environmental Sciences and Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mohit Jain
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Susan Cheng
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics & Environmental Sciences and Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Morgan E Grams
- Division of Precision Medicine, New York University School of Medicine, New York, NY, USA.
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
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Sieckmann T, Schley G, Ögel N, Kelterborn S, Boivin FJ, Fähling M, Ashraf MI, Reichel M, Vigolo E, Hartner A, Lichtenberger FB, Breiderhoff T, Knauf F, Rosenberger C, Aigner F, Schmidt-Ott K, Scholz H, Kirschner KM. Strikingly conserved gene expression changes of polyamine regulating enzymes among various forms of acute and chronic kidney injury. Kidney Int 2023; 104:90-107. [PMID: 37121432 DOI: 10.1016/j.kint.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023]
Abstract
The polyamines spermidine and spermine and their common precursor molecule putrescine are involved in tissue injury and repair. Here, we test the hypothesis that impaired polyamine homeostasis contributes to various kidney pathologies in mice during experimental models of ischemia-reperfusion, transplantation, rhabdomyolysis, cyclosporine treatment, arterial hypertension, diabetes, unilateral ureteral obstruction, high oxalate feeding, and adenine-induced injuries. We found a remarkably similar pattern in most kidney pathologies with reduced expression of enzymes involved in polyamine synthesis together with increased expression of polyamine degrading enzymes. Transcript levels of amine oxidase copper-containing 1 (Aoc1), an enzyme which catalyzes the breakdown of putrescine, were barely detectable by in situ mRNA hybridization in healthy kidneys. Aoc1 was highly expressed upon various experimental kidney injuries resulting in a significant reduction of kidney putrescine content. Kidney levels of spermine were also significantly reduced, whereas spermidine was increased in response to ischemia-reperfusion injury. Increased Aoc1 expression in injured kidneys was mainly accounted for by an Aoc1 isoform that harbors 22 additional amino acids at its N-terminus and shows increased secretion. Mice with germline deletion of Aoc1 and injured kidneys showed no decrease of kidney putrescine content; although they displayed no overt phenotype, they had fewer tubular casts upon ischemia-reperfusion injury. Hyperosmotic stress stimulated AOC1 expression at the transcriptional and post-transcription levels in metanephric explants and kidney cell lines. AOC1 expression was also significantly enhanced after kidney transplantation in humans. These data demonstrate that the kidneys respond to various forms of injury with down-regulation of polyamine synthesis and activation of the polyamine breakdown pathway. Thus, an imbalance in kidney polyamines may contribute to various etiologies of kidney injury.
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Affiliation(s)
- Tobias Sieckmann
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gunnar Schley
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Neslihan Ögel
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Simon Kelterborn
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix J Boivin
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michael Fähling
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Muhammad I Ashraf
- Department of Surgery, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Reichel
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Emilia Vigolo
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Andrea Hartner
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Falk-Bach Lichtenberger
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tilman Breiderhoff
- Department of Pediatrics, Division of Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christian Rosenberger
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix Aigner
- Department of Surgery, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Department of Surgery, St. John of God Hospital Graz, Graz, Austria
| | - Kai Schmidt-Ott
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Holger Scholz
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Karin M Kirschner
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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9
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Schlosser P, Scherer N, Grundner-Culemann F, Monteiro-Martins S, Haug S, Steinbrenner I, Uluvar B, Wuttke M, Cheng Y, Ekici AB, Gyimesi G, Karoly ED, Kotsis F, Mielke J, Gomez MF, Yu B, Grams ME, Coresh J, Boerwinkle E, Köttgen M, Kronenberg F, Meiselbach H, Mohney RP, Akilesh S, Schmidts M, Hediger MA, Schultheiss UT, Eckardt KU, Oefner PJ, Sekula P, Li Y, Köttgen A. Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine. Nat Genet 2023:10.1038/s41588-023-01409-8. [PMID: 37277652 DOI: 10.1038/s41588-023-01409-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
The kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies of paired plasma and urine metabolomes may identify underlying processes. We conducted genome-wide studies of 1,916 plasma and urine metabolites and detected 1,299 significant associations. Associations with 40% of implicated metabolites would have been missed by studying plasma alone. We detected urine-specific findings that provide information about metabolite reabsorption in the kidney, such as aquaporin (AQP)-7-mediated glycerol transport, and different metabolomic footprints of kidney-expressed proteins in plasma and urine that are consistent with their localization and function, including the transporters NaDC3 (SLC13A3) and ASBT (SLC10A2). Shared genetic determinants of 7,073 metabolite-disease combinations represent a resource to better understand metabolic diseases and revealed connections of dipeptidase 1 with circulating digestive enzymes and with hypertension. Extending genetic studies of the metabolome beyond plasma yields unique insights into processes at the interface of body compartments.
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Affiliation(s)
- Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Nora Scherer
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Sara Monteiro-Martins
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefan Haug
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Burulça Uluvar
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | | | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Johanna Mielke
- Research and Early Development, Pharmaceuticals Division, Bayer AG, Wuppertal, Germany
| | - Maria F Gomez
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Lund, Sweden
| | - Bing Yu
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Morgan E Grams
- New York University Grossman School of Medicine, New York, NY, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eric Boerwinkle
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Köttgen
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Miriam Schmidts
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Freiburg University Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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10
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Schachtl-Riess JF, Schönherr S, Lamina C, Forer L, Coassin S, Streiter G, Kheirkhah A, Li Y, Meiselbach H, Di Maio S, Eckardt KU, Köttgen A, Kronenberg F. KLKB1 and CLSTN2 are associated with HDL-mediated cholesterol efflux capacity in a genome-wide association study. Atherosclerosis 2023; 368:1-11. [PMID: 36812656 DOI: 10.1016/j.atherosclerosis.2023.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/06/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS HDL-mediated cholesterol efflux capacity (CEC) may protect from cardiovascular disease. Thus, we aimed to identify its genetic and non-genetic determinants. METHODS We measured CEC to 2% apolipoprotein B-depleted serum using BODIPY-cholesterol and cAMP-stimulated J774A.1 macrophages using serum samples from 4,981 participants in the German Chronic Kidney Disease (GCKD) study. Variance of CEC explained by clinical and biochemical parameters in a multivariable linear regression model was calculated by proportional marginal variance decomposition. A genome-wide association study with 7,746,917 variants was performed based on an additive genetic model. The main model was adjusted for age, sex and principal components 1-10. Further models were selected for sensitivity analysis and to reduce residual variance by known CEC pathways. RESULTS Variables that explained 1% and more of the variance of CEC were concentrations of triglycerides (12.9%), HDL-cholesterol (11.8%), LDL-cholesterol (3.0%), apolipoprotein A-IV (2.8%), PCSK9 (1.0%), and eGFR (1.0%). The KLKB1 (chr4) and APOE/C1 (chr19) loci were genome-wide significantly (p < 5x10-8) associated with CEC in our main model (p = 8.8x10-10 and p = 3.3x10-10, respectively). KLKB1 remained significantly associated after additional adjustment for either kidney parameters, HDL-cholesterol, triglycerides or apolipoprotein A-IV concentrations, while the APOE/C1 locus was not significantly associated anymore after adjustment for triglycerides. Adjustment for triglycerides also revealed an association with the CLSTN2 locus (chr3; p = 6.0x10-9). CONCLUSIONS We identified HDL-cholesterol and triglycerides as the main determinants of CEC. Furthermore, we newly found a significant association of CEC with the KLKB1 and the CLSTN2 locus and confirmed the association with the APOE/C1 locus, likely mediated by triglycerides.
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Affiliation(s)
- Johanna F Schachtl-Riess
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Gertraud Streiter
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Azin Kheirkhah
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Silvia Di Maio
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria.
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11
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Pfau A, López-Cayuqueo KI, Scherer N, Wuttke M, Wernstedt A, González Fassrainer D, Smith DE, van de Kamp JM, Ziegeler K, Eckardt KU, Luft FC, Aronson PS, Köttgen A, Jentsch TJ, Knauf F. SLC26A1 is a major determinant of sulfate homeostasis in humans. J Clin Invest 2023; 133:e161849. [PMID: 36719378 PMCID: PMC9888379 DOI: 10.1172/jci161849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/29/2022] [Indexed: 02/01/2023] Open
Abstract
Sulfate plays a pivotal role in numerous physiological processes in the human body, including bone and cartilage health. A role of the anion transporter SLC26A1 (Sat1) for sulfate reabsorption in the kidney is supported by the observation of hyposulfatemia and hypersulfaturia in Slc26a1-knockout mice. The impact of SLC26A1 on sulfate homeostasis in humans remains to be defined. By combining clinical genetics, functional expression assays, and population exome analysis, we identify SLC26A1 as a sulfate transporter in humans and experimentally validate several loss-of-function alleles. Whole-exome sequencing from a patient presenting with painful perichondritis, hyposulfatemia, and renal sulfate wasting revealed a homozygous mutation in SLC26A1, which has not been previously described to the best of our knowledge. Whole-exome data analysis of more than 5,000 individuals confirmed that rare, putatively damaging SCL26A1 variants were significantly associated with lower plasma sulfate at the population level. Functional expression assays confirmed a substantial reduction in sulfate transport for the SLC26A1 mutation of our patient, which we consider to be novel, as well as for the additional variants detected in the population study. In conclusion, combined evidence from 3 complementary approaches supports SLC26A1 activity as a major determinant of sulfate homeostasis in humans. In view of recent evidence linking sulfate homeostasis with back pain and intervertebral disc disorder, our study identifies SLC26A1 as a potential target for modulation of musculoskeletal health.
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Affiliation(s)
- Anja Pfau
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karen I. López-Cayuqueo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Nora Scherer
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center and
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center and
| | | | | | - Desiree E.C. Smith
- Metabolic Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience and
| | - Jiddeke M. van de Kamp
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Katharina Ziegeler
- Department of Radiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Friedrich C. Luft
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter S. Aronson
- Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center and
- CIBSS – Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
- NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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Bächle H, Sekula P, Schlosser P, Steinbrenner I, Cheng Y, Kotsis F, Meiselbach H, Stockmann H, Schönherr S, Eckardt KU, Devuyst O, Scherberich J, Köttgen A, Schultheiss UT. Uromodulin and its association with urinary metabolites: the German Chronic Kidney Disease Study. Nephrol Dial Transplant 2023; 38:70-79. [PMID: 35612992 DOI: 10.1093/ndt/gfac187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The progression of chronic kidney disease (CKD), a global public health burden, is accompanied by a declining number of functional nephrons. Estimation of remaining nephron mass may improve assessment of CKD progression. Uromodulin has been suggested as a marker of tubular mass. We aimed to identify metabolites associated with uromodulin concentrations in urine and serum to characterize pathophysiologic alterations of metabolic pathways to generate new hypotheses regarding CKD pathophysiology. METHODS We measured urinary and serum uromodulin levels (uUMOD, sUMOD) and 607 urinary metabolites and performed cross-sectional analyses within the German Chronic Kidney Disease study (N = 4628), a prospective observational study. Urinary metabolites significantly associated with uUMOD and sUMOD were used to build weighted metabolite scores for urine (uMS) and serum uromodulin (sMS) and evaluated for time to adverse kidney events over 6.5 years. RESULTS Metabolites cross-sectionally associated with uromodulin included amino acids of the tryptophan metabolism, lipids and nucleotides. Higher levels of the sMS [hazard ratio (HR) = 0.73 (95% confidence interval 0.64; 0.82), P = 7.45e-07] and sUMOD [HR = 0.74 (95% confidence interval 0.63; 0.87), P = 2.32e-04] were associated with a lower risk of adverse kidney events over time, whereas uUMOD and uMS showed the same direction of association but were not significant. CONCLUSIONS We identified urinary metabolites associated with urinary and serum uromodulin. The sUMOD and the sMS were associated with lower risk of adverse kidney events among CKD patients. Higher levels of sUMOD and sMS may reflect a higher number of functional nephrons and therefore a reduced risk of adverse kidney outcomes.
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Affiliation(s)
- Helena Bächle
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany.,Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Helena Stockmann
- Department of Nephrology and Medical Intensive Care, Charité, University-Medicine, Berlin, Germany
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Department of Nephrology and Medical Intensive Care, Charité, University-Medicine, Berlin, Germany
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Jürgen Scherberich
- Klinikum München-Harlaching, Nephrology & Clinical Immunology, Teaching Hospital of the Ludwig-Maximilians-University München, Munich, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany.,Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
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13
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Maaliki D, Itani MM, Itani HA. Pathophysiology and genetics of salt-sensitive hypertension. Front Physiol 2022; 13:1001434. [PMID: 36176775 PMCID: PMC9513236 DOI: 10.3389/fphys.2022.1001434] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Most hypertensive cases are primary and heavily associated with modifiable risk factors like salt intake. Evidence suggests that even small reductions in salt consumption reduce blood pressure in all age groups. In that regard, the ACC/AHA described a distinct set of individuals who exhibit salt-sensitivity, regardless of their hypertensive status. Data has shown that salt-sensitivity is an independent risk factor for cardiovascular events and mortality. However, despite extensive research, the pathogenesis of salt-sensitive hypertension is still unclear and tremendously challenged by its multifactorial etiology, complicated genetic influences, and the unavailability of a diagnostic tool. So far, the important roles of the renin-angiotensin-aldosterone system, sympathetic nervous system, and immune system in the pathogenesis of salt-sensitive hypertension have been studied. In the first part of this review, we focus on how the systems mentioned above are aberrantly regulated in salt-sensitive hypertension. We follow this with an emphasis on genetic variants in those systems that are associated with and/or increase predisposition to salt-sensitivity in humans.
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Affiliation(s)
- Dina Maaliki
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Maha M. Itani
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hana A. Itani
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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14
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Rinschen MM, Palygin O, El-Meanawy A, Domingo-Almenara X, Palermo A, Dissanayake LV, Golosova D, Schafroth MA, Guijas C, Demir F, Jaegers J, Gliozzi ML, Xue J, Hoehne M, Benzing T, Kok BP, Saez E, Bleich M, Himmerkus N, Weisz OA, Cravatt BF, Krüger M, Benton HP, Siuzdak G, Staruschenko A. Accelerated lysine metabolism conveys kidney protection in salt-sensitive hypertension. Nat Commun 2022; 13:4099. [PMID: 35835746 PMCID: PMC9283537 DOI: 10.1038/s41467-022-31670-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/27/2022] [Indexed: 01/07/2023] Open
Abstract
Hypertension and kidney disease have been repeatedly associated with genomic variants and alterations of lysine metabolism. Here, we combined stable isotope labeling with untargeted metabolomics to investigate lysine's metabolic fate in vivo. Dietary 13C6 labeled lysine was tracked to lysine metabolites across various organs. Globally, lysine reacts rapidly with molecules of the central carbon metabolism, but incorporates slowly into proteins and acylcarnitines. Lysine metabolism is accelerated in a rat model of hypertension and kidney damage, chiefly through N-alpha-mediated degradation. Lysine administration diminished development of hypertension and kidney injury. Protective mechanisms include diuresis, further acceleration of lysine conjugate formation, and inhibition of tubular albumin uptake. Lysine also conjugates with malonyl-CoA to form a novel metabolite Nε-malonyl-lysine to deplete malonyl-CoA from fatty acid synthesis. Through conjugate formation and excretion as fructoselysine, saccharopine, and Nε-acetyllysine, lysine lead to depletion of central carbon metabolites from the organism and kidney. Consistently, lysine administration to patients at risk for hypertension and kidney disease inhibited tubular albumin uptake, increased lysine conjugate formation, and reduced tricarboxylic acid (TCA) cycle metabolites, compared to kidney-healthy volunteers. In conclusion, lysine isotope tracing mapped an accelerated metabolism in hypertension, and lysine administration could protect kidneys in hypertensive kidney disease.
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Affiliation(s)
- Markus M Rinschen
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- III. Medical Clinic, University Hospital Hamburg Eppendorf, Hamburg, Germany.
- AIAS, Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark.
| | - Oleg Palygin
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ashraf El-Meanawy
- Division of Nephrology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Xavier Domingo-Almenara
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA
- Omics Sciences Unit, EURECAT, Technology Centre of Catalonia, Reus, Catalonia, Spain
| | - Amelia Palermo
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Lashodya V Dissanayake
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, 33602, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Daria Golosova
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | - Carlos Guijas
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA
| | - Fatih Demir
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Megan L Gliozzi
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jingchuan Xue
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA
| | - Martin Hoehne
- Center for Molecular Medicine Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department II of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Thomas Benzing
- Center for Molecular Medicine Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department II of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Bernard P Kok
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Enrique Saez
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Markus Bleich
- Institute of Physiology, University Kiel, Kiel, Germany
| | | | - Ora A Weisz
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | | | - Marcus Krüger
- Center for Molecular Medicine Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
| | - H Paul Benton
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA
| | - Gary Siuzdak
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA, 92037, USA.
| | - Alexander Staruschenko
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, 33602, USA.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- James A. Haley Veterans' Hospital, Tampa, FL, 33612, USA.
- Hypertension and Kidney Research Center, University of South Florida, Tampa, FL, 33602, USA.
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15
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Liu C, Wang Z, Hui Q, Chiang Y, Chen J, Brijkumar J, Edwards JA, Ordonez CE, Dudgeon MR, Sunpath H, Pillay S, Moodley P, Kuritzkes DR, Moosa MYS, Jones DP, Marconi VC, Sun YV. Crosstalk between Host Genome and Metabolome among People with HIV in South Africa. Metabolites 2022; 12:metabo12070624. [PMID: 35888748 PMCID: PMC9316179 DOI: 10.3390/metabo12070624] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/16/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association studies (GWAS) of circulating metabolites have revealed the role of genetic regulation on the human metabolome. Most previous investigations focused on European ancestry, and few studies have been conducted among populations of African descent living in Africa, where the infectious disease burden is high (e.g., human immunodeficiency virus (HIV)). It is important to understand the genetic associations of the metabolome in diverse at-risk populations including people with HIV (PWH) living in Africa. After a thorough literature review, the reported significant gene−metabolite associations were tested among 490 PWH in South Africa. Linear regression was used to test associations between the candidate metabolites and genetic variants. GWAS of 154 plasma metabolites were performed to identify novel genetic associations. Among the 29 gene−metabolite associations identified in the literature, we replicated 10 in South Africans with HIV. The UGT1A cluster was associated with plasma levels of biliverdin and bilirubin; SLC16A9 and CPS1 were associated with carnitine and creatine, respectively. We also identified 22 genetic associations with metabolites using a genome-wide significance threshold (p-value < 5 × 10−8). In a GWAS of plasma metabolites in South African PWH, we replicated reported genetic associations across ancestries, and identified novel genetic associations using a metabolomics approach.
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Affiliation(s)
- Chang Liu
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA; (C.L.); (Q.H.); (Y.C.); (J.C.)
| | - Zicheng Wang
- College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA;
| | - Qin Hui
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA; (C.L.); (Q.H.); (Y.C.); (J.C.)
| | - Yiyun Chiang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA; (C.L.); (Q.H.); (Y.C.); (J.C.)
| | - Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA; (C.L.); (Q.H.); (Y.C.); (J.C.)
| | - Jaysingh Brijkumar
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (J.B.); (H.S.); (S.P.); (M.Y.S.M.)
| | - Johnathan A. Edwards
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
- School of Medicine, Emory University, Atlanta, GA 30322, USA; (M.R.D.); (D.P.J.); (V.C.M.)
- Lincoln International Institute for Rural Health, School of Health and Social Care, University of Lincoln, Lincoln LN6 7TS, UK
| | - Claudia E. Ordonez
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - Mathew R. Dudgeon
- School of Medicine, Emory University, Atlanta, GA 30322, USA; (M.R.D.); (D.P.J.); (V.C.M.)
| | - Henry Sunpath
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (J.B.); (H.S.); (S.P.); (M.Y.S.M.)
| | - Selvan Pillay
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (J.B.); (H.S.); (S.P.); (M.Y.S.M.)
| | - Pravi Moodley
- National Health Laboratory Service, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4011, South Africa;
| | - Daniel R. Kuritzkes
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Mohamed Y. S. Moosa
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (J.B.); (H.S.); (S.P.); (M.Y.S.M.)
| | - Dean P. Jones
- School of Medicine, Emory University, Atlanta, GA 30322, USA; (M.R.D.); (D.P.J.); (V.C.M.)
| | - Vincent C. Marconi
- School of Medicine, Emory University, Atlanta, GA 30322, USA; (M.R.D.); (D.P.J.); (V.C.M.)
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
- Emory Vaccine Center, Atlanta, GA 30322, USA
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA; (C.L.); (Q.H.); (Y.C.); (J.C.)
- Correspondence: ; Tel.: +1-404-727-9090
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16
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Rhee EP, Surapaneni A, Zheng Z, Zhou L, Dutta D, Arking DE, Zhang J, Duong T, Chatterjee N, Luo S, Schlosser P, Mehta R, Waikar SS, Saraf SL, Kelly TN, Hamm LL, Rao PS, Mathew AV, Hsu CY, Parsa A, Vasan RS, Kimmel PL, Clish CB, Coresh J, Feldman HI, Grams ME. Trans-ethnic genome-wide association study of blood metabolites in the Chronic Renal Insufficiency Cohort (CRIC) study. Kidney Int 2022; 101:814-823. [PMID: 35120996 PMCID: PMC8940669 DOI: 10.1016/j.kint.2022.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/06/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
Abstract
Metabolomics genome wide association study (GWAS) help outline the genetic contribution to human metabolism. However, studies to date have focused on relatively healthy, population-based samples of White individuals. Here, we conducted a GWAS of 537 blood metabolites measured in the Chronic Renal Insufficiency Cohort (CRIC) Study, with separate analyses in 822 White and 687 Black study participants. Trans-ethnic meta-analysis was then applied to improve fine-mapping of potential causal variants. Mean estimated glomerular filtration rate was 44.4 and 41.5 mL/min/1.73m2 in the White and Black participants, respectively. There were 45 significant metabolite associations at 19 loci, including novel associations at PYROXD2, PHYHD1, FADS1-3, ACOT2, MYRF, FAAH, and LIPC. The strength of associations was unchanged in models additionally adjusted for estimated glomerular filtration rate and proteinuria, consistent with a direct biochemical effect of gene products on associated metabolites. At several loci, trans-ethnic meta-analysis, which leverages differences in linkage disequilibrium across populations, reduced the number and/or genomic interval spanned by potentially causal single nucleotide polymorphisms compared to fine-mapping in the White participant cohort alone. Across all validated associations, we found strong concordance in effect sizes of the potentially causal single nucleotide polymorphisms between White and Black study participants. Thus, our study identifies novel genetic determinants of blood metabolites in chronic kidney disease, demonstrates the value of diverse cohorts to improve causal inference in metabolomics GWAS, and underscores the shared genetic basis of metabolism across race.
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Affiliation(s)
- Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachussetts, USA.
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Diptavo Dutta
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jingning Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - ThuyVy Duong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Shengyuan Luo
- Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Rupal Mehta
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University School of Medicine, Boston Medical Center, Boston, Massachussetts, USA
| | - Santosh L Saraf
- Division of Hematology and Oncology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Lee L Hamm
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Panduranga S Rao
- Division of Nephrology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Anna V Mathew
- Division of Nephrology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Chi-Yuan Hsu
- Division of Nephrology, University of California, San Francisco School of Medicine, San Francisco, California, USA
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ramachandran S Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, Massachussetts, USA; Section of Cardiology, Department of Medicine, Boston University School of Medicine, Boston, Massachussetts, USA; Department of Epidemiology, Boston University School of Public Health, Boston, Massachussetts, USA
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Harold I Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA; Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
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17
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Cheng Y, Li Y, Scherer N, Grundner-Culemann F, Lehtimäki T, Mishra BH, Raitakari OT, Nauck M, Eckardt KU, Sekula P, Schultheiss UT. Genetics of osteopontin in patients with chronic kidney disease: The German Chronic Kidney Disease study. PLoS Genet 2022; 18:e1010139. [PMID: 35385482 PMCID: PMC9015153 DOI: 10.1371/journal.pgen.1010139] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/18/2022] [Accepted: 03/09/2022] [Indexed: 11/18/2022] Open
Abstract
Osteopontin (OPN), encoded by SPP1, is a phosphorylated glycoprotein predominantly synthesized in kidney tissue. Increased OPN mRNA and protein expression correlates with proteinuria, reduced creatinine clearance, and kidney fibrosis in animal models of kidney disease. But its genetic underpinnings are incompletely understood. We therefore conducted a genome-wide association study (GWAS) of OPN in a European chronic kidney disease (CKD) population. Using data from participants of the German Chronic Kidney Disease (GCKD) study (N = 4,897), a GWAS (minor allele frequency [MAF]≥1%) and aggregated variant testing (AVT, MAF<1%) of ELISA-quantified serum OPN, adjusted for age, sex, estimated glomerular filtration rate (eGFR), and urinary albumin-to-creatinine ratio (UACR) was conducted. In the project, GCKD participants had a mean age of 60 years (SD 12), median eGFR of 46 mL/min/1.73m2 (p25: 37, p75: 57) and median UACR of 50 mg/g (p25: 9, p75: 383). GWAS revealed 3 loci (p<5.0E-08), two of which replicated in the population-based Young Finns Study (YFS) cohort (p<1.67E-03): rs10011284, upstream of SPP1 encoding the OPN protein and related to OPN production, and rs4253311, mapping into KLKB1 encoding prekallikrein (PK), which is processed to kallikrein (KAL) implicated through the kinin-kallikrein system (KKS) in blood pressure control, inflammation, blood coagulation, cancer, and cardiovascular disease. The SPP1 gene was also identified by AVT (p = 2.5E-8), comprising 7 splice-site and missense variants. Among others, downstream analyses revealed colocalization of the OPN association signal at SPP1 with expression in pancreas tissue, and at KLKB1 with various plasma proteins in trans, and with phenotypes (bone disorder, deep venous thrombosis) in human tissue. In summary, this GWAS of OPN levels revealed two replicated associations. The KLKB1 locus connects the function of OPN with PK, suggestive of possible further post-translation processing of OPN. Further studies are needed to elucidate the complex role of OPN within human (patho)physiology.
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Affiliation(s)
- Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
| | - Nora Scherer
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Binisha H. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, 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
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité, University-Medicine, Berlin, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
| | - Ulla T. Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
- Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
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18
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Hu JR, Myint L, Levey AS, Coresh J, Inker LA, Grams ME, Guallar E, Hansen KD, Rhee EP, Shafi T. A metabolomics approach identified toxins associated with uremic symptoms in advanced chronic kidney disease. Kidney Int 2022; 101:369-378. [PMID: 34843755 PMCID: PMC8792216 DOI: 10.1016/j.kint.2021.10.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 02/03/2023]
Abstract
Uremic symptoms are common in patients with advanced chronic kidney disease, but the toxins that cause these symptoms are unknown. To evaluate this, we performed a cross-sectional study of the 12 month post-randomization follow-up visit of Modification of Diet in Renal Disease (MDRD) participants reporting uremic symptoms who also had available stored serum. We quantified 1,163 metabolites by liquid chromatography-tandem mass spectrometry. For each uremic symptom, we calculated a score as the severity multiplied by the number of days the symptom was experienced. We analyzed the associations of the individual symptom scores with metabolites using linear models with empirical Bayesian inference, adjusted for multiple comparisons. Among 695 participants, the mean measured glomerular filtration rate (mGFR) was 28 mL/min/1.73 m2. Uremic symptoms were more common in the subgroup of 214 patients with an mGFR under 20 mL/min/1.73 m2 (mGFR under 20 subgroup) than in the full group. For all metabolites with significant associations, the direction of the association was concordant in the full group and the subgroup. For gastrointestinal symptoms (bad taste, loss of appetite, nausea, and vomiting), eleven metabolites were associated with symptoms. For neurologic symptoms (decreased alertness, falling asleep during the day, forgetfulness, lack of pep and energy, and tiring easily/weakness), seven metabolites were associated with symptoms. Associations were consistent across sensitivity analyses. Thus, our proof-of-principle study demonstrates the potential for metabolomics to understand metabolic pathways associated with uremic symptoms. Larger, prospective studies with external validation are needed.
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Affiliation(s)
- Jiun-Ruey Hu
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Leslie Myint
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN
| | | | - Josef Coresh
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Morgan E. Grams
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University School of Medicine, Baltimore, MD,Division of Nephrology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Eliseo Guallar
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kasper D. Hansen
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Eugene P. Rhee
- Division of Nephrology, Massachussetts General Hospital, Boston, MA
| | - Tariq Shafi
- Division of Nephrology, University of Mississippi Medical Center, Jackson, MS
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19
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Hysi PG, Mangino M, Christofidou P, Falchi M, Karoly ED, Mohney RP, Valdes AM, Spector TD, Menni C. Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels. Metabolites 2022; 12:61. [PMID: 35050183 PMCID: PMC8777659 DOI: 10.3390/metabo12010061] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/27/2023] Open
Abstract
Metabolites are small products of metabolism that provide a snapshot of the wellbeing of an organism and the mechanisms that control key physiological processes involved in health and disease. Here we report the results of a genome-wide association study of 722 circulating metabolite levels in 8809 subjects of European origin, providing both breadth and depth. These analyses identified 202 unique genomic regions whose variations are associated with the circulating levels of 478 different metabolites. Replication with a subset of 208 metabolites that were available in an independent dataset for a cohort of 1768 European subjects confirmed the robust associations, including 74 novel genomic regions not associated with any metabolites in previous works. This study enhances our knowledge of genetic mechanisms controlling human metabolism. Our findings have major potential for identifying novel targets and developing new therapeutic strategies.
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Affiliation(s)
- Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
- NIHR Biomedical Research Centre at Guy’s and St. Thomas’ Foundation Trust, London SE1 9RT, UK
| | - Paraskevi Christofidou
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
| | - Edward D. Karoly
- Discovery and Translational Sciences, Metabolon Inc., Raleigh-Durham, NC 27560, USA; (E.D.K.); (R.P.M.)
| | | | - Robert P. Mohney
- Discovery and Translational Sciences, Metabolon Inc., Raleigh-Durham, NC 27560, USA; (E.D.K.); (R.P.M.)
| | - Ana M. Valdes
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
- Inflammation, Injury and Recovery Sciences, School of Medicine, University of Nottingham, Nottingham NG5 1PB, UK
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK; (P.G.H.); (M.M.); (P.C.); (M.F.); (A.M.V.)
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20
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Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021; 12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic syndrome (MetS) is a highly heritable disease and a major public health burden worldwide. MetS diagnosis criteria are met by the simultaneous presence of any three of the following: high triglycerides, low HDL/high LDL cholesterol, insulin resistance, hypertension, and central obesity. These diseases act synergistically in people suffering from MetS and dramatically increase risk of morbidity and mortality due to stroke and cardiovascular disease, as well as certain cancers. Each of these component features is itself a complex disease, as is MetS. As a genetically complex disease, genetic risk factors for MetS are numerous, but not very powerful individually, often requiring specific environmental stressors for the disease to manifest. When taken together, all sequence variants that contribute to MetS disease risk explain only a fraction of the heritable variance, suggesting additional, novel loci have yet to be discovered. In this article, we will give a brief overview on the genetic concepts needed to interpret genome-wide association studies (GWAS) and quantitative trait locus (QTL) data, summarize the state of the field of MetS physiological genomics, and to introduce tools and resources that can be used by the physiologist to integrate genomics into their own research on MetS and any of its component features. There is a wealth of phenotypic and molecular data in animal models and humans that can be leveraged as outlined in this article. Integrating these multi-omic QTL data for complex diseases such as MetS provides a means to unravel the pathways and mechanisms leading to complex disease and promise for novel treatments. © 2022 American Physiological Society. Compr Physiol 12:1-40, 2022.
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Affiliation(s)
- Karen C Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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21
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Luo S, Feofanova EV, Tin A, Tung S, Rhee EP, Coresh J, Arking DE, Surapaneni A, Schlosser P, Li Y, Köttgen A, Yu B, Grams ME. Genome-wide association study of serum metabolites in the African American Study of Kidney Disease and Hypertension. Kidney Int 2021; 100:430-439. [PMID: 33838163 PMCID: PMC8583323 DOI: 10.1016/j.kint.2021.03.026] [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: 08/10/2020] [Revised: 02/26/2021] [Accepted: 03/11/2021] [Indexed: 01/23/2023]
Abstract
The genome-wide association study (GWAS) is a powerful means to study genetic determinants of disease traits and generate insights into disease pathophysiology. To date, few GWAS of circulating metabolite levels have been performed in African Americans with chronic kidney disease. Hypothesizing that novel genetic-metabolite associations may be identified in a unique population of African Americans with a lower glomerular filtration rate (GFR), we conducted a GWAS of 652 serum metabolites in 619 participants (mean measured glomerular filtration rate 45 mL/min/1.73m2) in the African American Study of Kidney Disease and Hypertension, a clinical trial of blood pressure lowering and antihypertensive medication in African Americans with chronic kidney disease. We identified 42 significant variant metabolite associations. Twenty associations had been previously identified in published GWAS, and eleven novel associations were replicated in a separate cohort of 818 African Americans with genetic and metabolomic data from the Atherosclerosis Risk in Communities Study. The replicated novel variant-metabolite associations comprised eight metabolites and eleven distinct genomic loci. Nine of the replicated associations represented clear enzyme-metabolite interactions, with high expression in the kidneys as well as the liver. Three loci (ACY1, ACY3, and NAT8) were associated with a common pool of metabolites, acetylated amino acids, but with different individual affinities. Thus, extensive metabolite profiling in an African American population with chronic kidney disease aided identification of novel genome-wide metabolite associations, providing clues about substrate specificity and the key roles of enzymes in modulating systemic levels of metabolites.
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Affiliation(s)
- Shengyuan Luo
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA.
| | - Elena V Feofanova
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah Tung
- Johns Hopkins Whiting School of Engineering, Baltimore, Maryland, USA
| | - Eugene P Rhee
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Bing Yu
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland, USA; Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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A Genome-Wide Association Study for Hypertensive Kidney Disease in Korean Men. Genes (Basel) 2021; 12:genes12050751. [PMID: 34067580 PMCID: PMC8155956 DOI: 10.3390/genes12050751] [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: 03/17/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 11/26/2022] Open
Abstract
Hypertension is one of the major risk factors for chronic kidney disease (CKD), and the coexistence of hypertension and CKD increases morbidity and mortality. Although many genetic factors have been identified separately for hypertension and kidney disease, studies specifically focused on hypertensive kidney disease (HKD) have been rare. Therefore, this study aimed to identify loci or genes associated with HKD. A genome-wide association study (GWAS) was conducted using two Korean cohorts, the Health Examinee (HEXA) and Korean Association REsource (KARE). Consequently, 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with HKD in the discovery and replication phases (p < 5 × 10−8, p < 0.05, respectively). We further analyzed HKD-related traits such as the estimated glomerular filtration rate (eGFR), creatinine, blood urea nitrogen (BUN), systolic blood pressure (SBP) and diastolic blood pressure (DBP) at the 14q21.2 locus, which showed a strong linkage disequilibrium (LD). Expression quantitative trait loci (eQTL) analysis was also performed to determine whether HKD-related SNPs affect gene expression changes in glomerular and arterial tissues. The results suggested that the FANCM gene may affect the development of HKD through an integrated analysis of eQTL and GWAS and was the most significantly associated candidate gene. Taken together, this study indicated that the FANCM gene is involved in the pathogenesis of HKD. Additionally, our results will be useful in prioritizing other genes for further experiments.
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Cheng Y, Schlosser P, Hertel J, Sekula P, Oefner PJ, Spiekerkoetter U, Mielke J, Freitag DF, Schmidts M, Kronenberg F, Eckardt KU, Thiele I, Li Y, Köttgen A. Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism. Nat Commun 2021; 12:964. [PMID: 33574263 PMCID: PMC7878905 DOI: 10.1038/s41467-020-20877-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
Metabolite levels in urine may provide insights into genetic mechanisms shaping their related pathways. We therefore investigate the cumulative contribution of rare, exonic genetic variants on urine levels of 1487 metabolites and 53,714 metabolite ratios among 4864 GCKD study participants. Here we report the detection of 128 significant associations involving 30 unique genes, 16 of which are known to underlie inborn errors of metabolism. The 30 genes are strongly enriched for shared expression in liver and kidney (odds ratio = 65, p-FDR = 3e-7), with hepatocytes and proximal tubule cells as driving cell types. Use of UK Biobank whole-exome sequencing data links genes to diseases connected to the identified metabolites. In silico constraint-based modeling of gene knockouts in a virtual whole-body, organ-resolved metabolic human correctly predicts the observed direction of metabolite changes, highlighting the potential of linking population genetics to modeling. Our study implicates candidate variants and genes for inborn errors of metabolism.
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Affiliation(s)
- Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
- University of Greifswald, University Medicine Greifswald, Department of Psychiatry and Psychotherapy, Greifswald, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Ute Spiekerkoetter
- Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Johanna Mielke
- Bayer AG, Division Pharmaceuticals, Open Innovation & Digital Technologies, Wuppertal, Germany
| | - Daniel F Freitag
- Bayer AG, Division Pharmaceuticals, Open Innovation & Digital Technologies, Wuppertal, Germany
| | - Miriam Schmidts
- Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
- Division of Microbiology, National University of Ireland, Galway, University Road, Galway, Ireland
- APC Microbiome Ireland, Galway, Ireland
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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25
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Luo S, Surapaneni A, Zheng Z, Rhee EP, Coresh J, Hung AM, Nadkarni GN, Yu B, Boerwinkle E, Tin A, Arking DE, Steinbrenner I, Schlosser P, Köttgen A, Grams ME. NAT8 Variants, N-Acetylated Amino Acids, and Progression of CKD. Clin J Am Soc Nephrol 2020; 16:37-47. [PMID: 33380473 PMCID: PMC7792648 DOI: 10.2215/cjn.08600520] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/04/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVES Genetic variants in NAT8, a liver- and kidney-specific acetyltransferase encoding gene, have been associated with eGFR and CKD in European populations. Higher circulating levels of two NAT8-associated metabolites, N-δ-acetylornithine and N-acetyl-1-methylhistidine, have been linked to lower eGFR and higher risk of incident CKD in the Black population. We aimed to expand upon prior studies to investigate associations between rs13538, a missense variant in NAT8, N-acetylated amino acids, and kidney failure in multiple, well-characterized cohorts. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We conducted analyses among participants with genetic and/or serum metabolomic data in the African American Study of Kidney Disease and Hypertension (AASK; n=962), the Atherosclerosis Risk in Communities (ARIC) study (n=1050), and BioMe, an electronic health record-linked biorepository (n=680). Separately, we evaluated associations between rs13538, urinary N-acetylated amino acids, and kidney failure in participants in the German CKD (GCKD) study (n=1624). RESULTS Of 31 N-acetylated amino acids evaluated, the circulating and urinary levels of 14 were associated with rs13538 (P<0.05/31). Higher circulating levels of five of these N-acetylated amino acids, namely, N-δ-acetylornithine, N-acetyl-1-methylhistidine, N-acetyl-3-methylhistidine, N-acetylhistidine, and N2,N5-diacetylornithine, were associated with kidney failure, after adjustment for confounders and combining results in meta-analysis (combined hazard ratios per two-fold higher amino acid levels: 1.48, 1.44, 1.21, 1.65, and 1.41, respectively; 95% confidence intervals: 1.21 to 1.81, 1.22 to 1.70, 1.08 to 1.37, 1.29 to 2.10, and 1.17 to 1.71, respectively; all P values <0.05/14). None of the urinary levels of these N-acetylated amino acids were associated with kidney failure in the GCKD study. CONCLUSIONS We demonstrate significant associations between an NAT8 gene variant and 14 N-acetylated amino acids, five of which had circulation levels that were associated with kidney failure.
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Affiliation(s)
- Shengyuan Luo
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Eugene P. Rhee
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Adriana M. Hung
- Geriatric Research Education Clinical Center, Veteran Administration Tennessee Valley Health Care System, Nashville, Tennessee
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Girish N. Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Sciences Center at Houston School of Public Health, Houston, Texas
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Sciences Center at Houston School of Public Health, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
- Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
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26
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Gillenwater LA, Pratte KA, Hobbs BD, Cho MH, Zhuang Y, Halper-Stromberg E, Cruickshank-Quinn C, Reisdorph N, Petrache I, Labaki WW, O'Neal WK, Ortega VE, Jones DP, Uppal K, Jacobson S, Michelotti G, Wendt CH, Kechris KJ, Bowler RP. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. NETWORK AND SYSTEMS MEDICINE 2020; 3:159-181. [PMID: 33987620 PMCID: PMC8109053 DOI: 10.1089/nsm.2020.0009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Small studies have recently suggested that there are specific plasma metabolic signatures in chronic obstructive pulmonary disease (COPD), but there have been no large comprehensive study of metabolomic signatures in COPD that also integrate genetic variants. Materials and Methods: Fresh frozen plasma from 957 non-Hispanic white subjects in COPDGene was used to quantify 995 metabolites with Metabolon's global metabolomics platform. Metabolite associations with five COPD phenotypes (chronic bronchitis, exacerbation frequency, percent emphysema, post-bronchodilator forced expiratory volume at one second [FEV1]/forced vital capacity [FVC], and FEV1 percent predicted) were assessed. A metabolome-wide association study was performed to find genetic associations with metabolite levels. Significantly associated single-nucleotide polymorphisms were tested for replication with independent metabolomic platforms and independent cohorts. COPD phenotype-driven modules were identified in network analysis integrated with genetic associations to assess gene-metabolite-phenotype interactions. Results: Of metabolites tested, 147 (14.8%) were significantly associated with at least 1 COPD phenotype. Associations with airflow obstruction were enriched for diacylglycerols and branched chain amino acids. Genetic associations were observed with 109 (11%) metabolites, 72 (66%) of which replicated in an independent cohort. For 20 metabolites, more than 20% of variance was explained by genetics. A sparse network of COPD phenotype-driven modules was identified, often containing metabolites missed in previous testing. Of the 26 COPD phenotype-driven modules, 6 contained metabolites with significant met-QTLs, although little module variance was explained by genetics. Conclusion: A dysregulation of systemic metabolism was predominantly found in COPD phenotypes characterized by airflow obstruction, where we identified robust heritable effects on individual metabolite abundances. However, network analysis, which increased the statistical power to detect associations missed previously in classic regression analyses, revealed that the genetic influence on COPD phenotype-driven metabolomic modules was modest when compared with clinical and environmental factors.
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Affiliation(s)
| | | | - Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Yonghua Zhuang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | | | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Irina Petrache
- National Jewish Health, Denver, Colorado, USA
- School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Wassim W. Labaki
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Wanda K. O'Neal
- Lung Institute/Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victor E. Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Dean P. Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, Georgia, USA
| | - Karan Uppal
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, Georgia, USA
| | | | | | - Christine H. Wendt
- Department of Medicine, University of Minnesota and the VAMC, Minneapolis, Minnesota, USA
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Russell P. Bowler
- National Jewish Health, Denver, Colorado, USA
- School of Medicine, University of Colorado, Aurora, Colorado, USA
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27
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Lei X, Tie J, Fujita H. Relational completion based non-negative matrix factorization for predicting metabolite-disease associations. Knowl Based Syst 2020. [DOI: 10.1016/j.knosys.2020.106238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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28
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Sekula P, Tin A, Schultheiss UT, Baid-Agrawal S, Mohney RP, Steinbrenner I, Yu B, Luo S, Boerwinkle E, Eckardt KU, Coresh J, Grams ME, Kӧttgen A. Urine 6-Bromotryptophan: Associations with Genetic Variants and Incident End-Stage Kidney Disease. Sci Rep 2020; 10:10018. [PMID: 32572055 PMCID: PMC7308283 DOI: 10.1038/s41598-020-66334-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/17/2020] [Indexed: 12/24/2022] Open
Abstract
Higher serum 6-bromotryptophan has been associated with lower risk of chronic kidney disease (CKD) progression, implicating mechanisms beyond renal clearance. We studied genetic determinants of urine 6-bromotryptophan and its association with CKD risk factors and incident end-stage kidney disease (ESKD) in 4,843 participants of the German Chronic Kidney Disease (GCKD) study. 6-bromotryptophan was measured from urine samples using mass spectrometry. Patients with higher levels of urine 6-bromotryptophan had higher baseline estimated glomerular filtration rate (eGFR, p < 0.001). A genome-wide association study of urine 6-bromotryptophan identified two significant loci possibly related to its tubular reabsorption, SLC6A19, and its production, ERO1A, which was also associated with serum 6-bromotryptophan in an independent study. The association between urine 6-bromotryptophan and time to ESKD was assessed using Cox regression. There were 216 ESKD events after four years of follow-up. Compared with patients with undetectable levels, higher 6-bromotryptophan levels were associated with lower risk of ESKD in models unadjusted and adjusted for ESKD risk factors other than eGFR (
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Affiliation(s)
- Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Adrienne Tin
- Division of Nephrology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- The Memory Impairment and Neurodegenerative Dementia Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Division of Nephrology, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Seema Baid-Agrawal
- Department of Nephrology and Transplant Center, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | | | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Bing Yu
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, USA
| | - Shengyuan Luo
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | - Eric Boerwinkle
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, USA
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anna Kӧttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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29
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Epidemiology research to foster improvement in chronic kidney disease care. Kidney Int 2020; 97:477-486. [DOI: 10.1016/j.kint.2019.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 11/24/2022]
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Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans. Nat Genet 2020; 52:167-176. [PMID: 31959995 DOI: 10.1038/s41588-019-0567-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 12/05/2019] [Indexed: 11/08/2022]
Abstract
The kidneys integrate information from continuous systemic processes related to the absorption, distribution, metabolism and excretion (ADME) of metabolites. To identify underlying molecular mechanisms, we performed genome-wide association studies of the urinary concentrations of 1,172 metabolites among 1,627 patients with reduced kidney function. The 240 unique metabolite-locus associations (metabolite quantitative trait loci, mQTLs) that were identified and replicated highlight novel candidate substrates for transport proteins. The identified genes are enriched in ADME-relevant tissues and cell types, and they reveal novel candidates for biotransformation and detoxification reactions. Fine mapping of mQTLs and integration with single-cell gene expression permitted the prioritization of causal genes, functional variants and target cell types. The combination of mQTLs with genetic and health information from 450,000 UK Biobank participants illuminated metabolic mediators, and hence, novel urinary biomarkers of disease risk. This comprehensive resource of genetic targets and their substrates is informative for ADME processes in humans and is relevant to basic science, clinical medicine and pharmaceutical research.
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31
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Pan G, Cavalli M, Carlsson B, Skrtic S, Kumar C, Wadelius C. rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression. iScience 2020; 23:100808. [PMID: 31928966 PMCID: PMC7033636 DOI: 10.1016/j.isci.2019.100808] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Long-chain polyunsaturated fatty acids (LC-PUFAs) influence human health in several areas, including cardiovascular disease, diabetes, fatty liver disease, and cancer. ELOVL2 encodes one of the key enzymes in the in vivo synthesis of LC-PUFAs from their precursors. Variants near ELOVL2 have repeatedly been associated with levels of LC-PUFA-derived metabolites in genome-wide association studies (GWAS), but the mechanisms behind these observations remain poorly defined. In this study, we found that rs953413, located in the first intron of ELOVL2, lies within a functional FOXA and HNF4α cooperative binding site. The G allele of rs953413 increases binding of FOXA1/FOXA2 and HNF4α to an evolutionarily conserved enhancer element, conferring allele-specific upregulation of the rs953413-associated gene ELOVL2. The expression of ELOVL2 was significantly downregulated by both FOXA1 and HNF4α knockdown and CRISPR/Cas9-mediated direct mutation to the enhancer element. Our results suggest that rs953413 regulates LC-PUFAs metabolism by altering ELOVL2 expression through FOXA1/FOXA2 and HNF4α cooperation. rs953413 resides in an evolutionarily conserved enhancer region rs953413 mediates the cooperative binding of FOXA and HNF4α to the enhancer region The rs953413 locus plays a key role in regulating ELOVL2 expression rs953413 is implicated in PUFA metabolism by regulating ELOVL2 expression
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Affiliation(s)
- Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Björn Carlsson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Stanko Skrtic
- Pharmaceutical Technology & Development, AstraZeneca AB, Gothenburg, Sweden; Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Chanchal Kumar
- Translational Science & Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; Karolinska Institutet/AstraZeneca Integrated CardioMetabolic Center (KI/AZ ICMC), Department of Medicine, Novum, Huddinge, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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32
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Feng YL, Cao G, Chen DQ, Vaziri ND, Chen L, Zhang J, Wang M, Guo Y, Zhao YY. Microbiome-metabolomics reveals gut microbiota associated with glycine-conjugated metabolites and polyamine metabolism in chronic kidney disease. Cell Mol Life Sci 2019; 76:4961-4978. [PMID: 31147751 PMCID: PMC11105293 DOI: 10.1007/s00018-019-03155-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/28/2019] [Accepted: 05/16/2019] [Indexed: 12/21/2022]
Abstract
Dysbiosis of the gut microbiome and related metabolites in chronic kidney disease (CKD) have been intimately associated with the prevalence of cardiovascular diseases. Unfortunately, thus far, there is a paucity of sufficient knowledge of gut microbiome and related metabolites on CKD progression partly due to the severely limited investigations. Using a 5/6 nephrectomized (NX) rat model, we carried out 16S rRNA sequence and untargeted metabolomic analyses to explore the relationship between colon's microbiota and serum metabolites. Marked decline in microbial diversity and richness was accompanied by significant changes in 291 serum metabolites, which were mediated by altered enzymatic activities and dysregulations of lipids, amino acids, bile acids and polyamines metabolisms. Interestingly, CCr was directly associated with some microbial genera and polyamine metabolism. However, SBP was directly related to certain microbial genera and glycine-conjugated metabolites in CKD rats. Administration of poricoic acid A (PAA) and Poria cocos (PC) ameliorated microbial dysbiosis as well as attenuated hypertension and renal fibrosis. In addition, treatments with PAA and PC lowered serum levels of microbial-derived products including glycine-conjugated compounds and polyamine metabolites. Collectively, the present study confirmed the CKD-associated gut microbial dysbiosis and identified a novel dietary and therapeutic strategy to improve the gut microbial dysbiosis and the associated metabolomic disorders and retarded the progression of kidney disease in the rat model of CKD.
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Affiliation(s)
- Ya-Long Feng
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Gang Cao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang, 310053, China
| | - Dan-Qian Chen
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Nosratola D Vaziri
- Division of Nephrology and Hypertension, School of Medicine, University of California Irvine, Irvine, CA, 92897, USA
| | - Lin Chen
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Jun Zhang
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Ming Wang
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Yan Guo
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ying-Yong Zhao
- School of Pharmacy, Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
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Odintsova VV, Hagenbeek FA, Suderman M, Caramaschi D, van Beijsterveldt CEM, Kallsen NA, Ehli EA, Davies GE, Sukhikh GT, Fanos V, Relton C, Bartels M, Boomsma DI, van Dongen J. DNA Methylation Signatures of Breastfeeding in Buccal Cells Collected in Mid-Childhood. Nutrients 2019; 11:E2804. [PMID: 31744183 PMCID: PMC6893543 DOI: 10.3390/nu11112804] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
Breastfeeding has long-term benefits for children that may be mediated via the epigenome. This pathway has been hypothesized, but the number of empirical studies in humans is small and mostly done by using peripheral blood as the DNA source. We performed an epigenome-wide association study (EWAS) in buccal cells collected around age nine (mean = 9.5) from 1006 twins recruited by the Netherlands Twin Register (NTR). An age-stratified analysis examined if effects attenuate with age (median split at 10 years; n<10 = 517, mean age = 7.9; n>10 = 489, mean age = 11.2). We performed replication analyses in two independent cohorts from the NTR (buccal cells) and the Avon Longitudinal Study of Parents and Children (ALSPAC) (peripheral blood), and we tested loci previously associated with breastfeeding in epigenetic studies. Genome-wide DNA methylation was assessed with the Illumina Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA, USA) in the NTR and with the HumanMethylation450 Bead Chip in the ALSPAC. The duration of breastfeeding was dichotomized ('never' vs. 'ever'). In the total sample, no robustly associated epigenome-wide significant CpGs were identified (α = 6.34 × 10-8). In the sub-group of children younger than 10 years, four significant CpGs were associated with breastfeeding after adjusting for child and maternal characteristics. In children older than 10 years, methylation differences at these CpGs were smaller and non-significant. The findings did not replicate in the NTR sample (n = 98; mean age = 7.5 years), and no nearby sites were associated with breastfeeding in the ALSPAC study (n = 938; mean age = 7.4). Of the CpG sites previously reported in the literature, three were associated with breastfeeding in children younger than 10 years, thus showing that these CpGs are associated with breastfeeding in buccal and blood cells. Our study is the first to show that breastfeeding is associated with epigenetic variation in buccal cells in children. Further studies are needed to investigate if methylation differences at these loci are caused by breastfeeding or by other unmeasured confounders, as well as what mechanism drives changes in associations with age.
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Affiliation(s)
- Veronika V. Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 101000, Russia
| | - Fiona A. Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol BS8 1TH, UK
| | - Doretta Caramaschi
- MRC Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol BS8 1TH, UK
| | | | - Noah A. Kallsen
- Avera Institute for Human Genetics, Sioux Falls, SD 57101, USA
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD 57101, USA
| | | | - Gennady T. Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 101000, Russia
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU and University of Cagliari, 09121 Cagliari, Italy
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol BS8 1TH, UK
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
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Saez-Rodriguez J, Rinschen MM, Floege J, Kramann R. Big science and big data in nephrology. Kidney Int 2019; 95:1326-1337. [PMID: 30982672 DOI: 10.1016/j.kint.2018.11.048] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/11/2018] [Accepted: 11/20/2018] [Indexed: 12/16/2022]
Abstract
There have been tremendous advances during the last decade in methods for large-scale, high-throughput data generation and in novel computational approaches to analyze these datasets. These advances have had a profound impact on biomedical research and clinical medicine. The field of genomics is rapidly developing toward single-cell analysis, and major advances in proteomics and metabolomics have been made in recent years. The developments on wearables and electronic health records are poised to change clinical trial design. This rise of 'big data' holds the promise to transform not only research progress, but also clinical decision making towards precision medicine. To have a true impact, it requires integrative and multi-disciplinary approaches that blend experimental, clinical and computational expertise across multiple institutions. Cancer research has been at the forefront of the progress in such large-scale initiatives, so-called 'big science,' with an emphasis on precision medicine, and various other areas are quickly catching up. Nephrology is arguably lagging behind, and hence these are exciting times to start (or redirect) a research career to leverage these developments in nephrology. In this review, we summarize advances in big data generation, computational analysis, and big science initiatives, with a special focus on applications to nephrology.
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Affiliation(s)
- Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany; Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany.
| | - Markus M Rinschen
- Department II of Internal Medicine, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Center for Mass Spectrometry and Metabolomics, The Scripps Research Institute, La Jolla, California, USA
| | - Jürgen Floege
- RWTH Aachen, Department of Nephrology and Clinical Immunology, Aachen, Germany
| | - Rafael Kramann
- RWTH Aachen, Department of Nephrology and Clinical Immunology, Aachen, Germany; Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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Affiliation(s)
- Lili Liu
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
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