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Cañadas-Garre M, Baños-Jaime B, Maqueda JJ, Smyth LJ, Cappa R, Skelly R, Hill C, Brennan EP, Doyle R, Godson C, Maxwell AP, McKnight AJ. Genetic variants affecting mitochondrial function provide further insights for kidney disease. BMC Genomics 2024; 25:576. [PMID: 38858654 PMCID: PMC11163707 DOI: 10.1186/s12864-024-10449-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a complex disorder that has become a high prevalence global health problem, with diabetes being its predominant pathophysiologic driver. Autosomal genetic variation only explains some of the predisposition to kidney disease. Variations in the mitochondrial genome (mtDNA) and nuclear-encoded mitochondrial genes (NEMG) are implicated in susceptibility to kidney disease and CKD progression, but they have not been thoroughly explored. Our aim was to investigate the association of variation in both mtDNA and NEMG with CKD (and related traits), with a particular focus on diabetes. METHODS We used the UK Biobank (UKB) and UK-ROI, an independent collection of individuals with type 1 diabetes mellitus (T1DM) patients. RESULTS Fourteen mitochondrial variants were associated with estimated glomerular filtration rate (eGFR) in UKB. Mitochondrial variants and haplogroups U, H and J were associated with eGFR and serum variables. Mitochondrial haplogroup H was associated with all the serum variables regardless of the presence of diabetes. Mitochondrial haplogroup X was associated with end-stage kidney disease (ESKD) in UKB. We confirmed the influence of several known NEMG on kidney disease and function and found novel associations for SLC39A13, CFL1, ACP2 or ATP5G1 with serum variables and kidney damage, and for SLC4A1, NUP210 and MYH14 with ESKD. The G allele of TBC1D32-rs113987180 was associated with higher risk of ESKD in patients with diabetes (OR:9.879; CI95%:4.440-21.980; P = 2.0E-08). In UK-ROI, AGXT2-rs71615838 and SURF1-rs183853102 were associated with diabetic nephropathies, and TFB1M-rs869120 with eGFR. CONCLUSIONS We identified novel variants both in mtDNA and NEMG which may explain some of the missing heritability for CKD and kidney phenotypes. We confirmed the role of MT-ND5 and mitochondrial haplogroup H on renal disease (serum variables), and identified the MT-ND5-rs41535848G variant, along with mitochondrial haplogroup X, associated with higher risk of ESKD. Despite most of the associations were independent of diabetes, we also showed potential roles for NEMG in T1DM.
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Affiliation(s)
- Marisa Cañadas-Garre
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK.
- Genomic Oncology Area, Centre for Genomics and Oncological Research: Pfizer, GENYO, University of Granada-Andalusian Regional Government, PTS Granada. Avenida de La Ilustración 114, 18016, Granada, Spain.
- Hematology Department, Hospital Universitario Virgen de Las Nieves, Avenida de Las Fuerzas Armadas 2, 18014, Granada, Spain.
- Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Avda. de Madrid, 15, 18012, Granada, Spain.
| | - Blanca Baños-Jaime
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja (cicCartuja), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla, Avda. Américo Vespucio 49, 41092, Seville, Spain
| | - Joaquín J Maqueda
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Experimental Oncology Laboratory, IRCCS Rizzoli Orthopaedic Institute, 40136, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Laura J Smyth
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Ruaidhri Cappa
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Ryan Skelly
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Claire Hill
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Eoin P Brennan
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ross Doyle
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
- Mater Misericordiae University Hospital, Eccles St, Dublin, D07 R2WY, Ireland
| | - Catherine Godson
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Alexander P Maxwell
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Level 11Lisburn Road, Belfast, BT9 7AB, UK
| | - Amy Jayne McKnight
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
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Greenhalgh R, Klure DM, Orr TJ, Armstrong NM, Shapiro MD, Dearing MD. The desert woodrat (Neotoma lepida) induces a diversity of biotransformation genes in response to creosote bush resin. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109870. [PMID: 38428625 PMCID: PMC11006593 DOI: 10.1016/j.cbpc.2024.109870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Liver biotransformation enzymes have long been thought to enable animals to feed on diets rich in xenobiotic compounds. However, despite decades of pharmacological research in humans and rodents, little is known about hepatic gene expression in specialized mammalian herbivores feeding on toxic diets. Leveraging a recently identified population of the desert woodrat (Neotoma lepida) found to be highly tolerant to toxic creosote bush (Larrea tridentata), we explored the expression changes of suites of biotransformation genes in response to diets enriched with varying amounts of creosote resin. Analysis of hepatic RNA-seq data indicated a dose-dependent response to these compounds, including the upregulation of several genes encoding transcription factors and numerous phase I, II, and III biotransformation families. Notably, elevated expression of five biotransformation families - carboxylesterases, cytochromes P450, aldo-keto reductases, epoxide hydrolases, and UDP-glucuronosyltransferases - corresponded to species-specific duplication events in the genome, suggesting that these genes play a prominent role in N. lepida's adaptation to creosote bush. Building on pharmaceutical studies in model rodents, we propose a hypothesis for how the differentially expressed genes are involved in the biotransformation of creosote xenobiotics. Our results provide some of the first details about how these processes likely operate in the liver of a specialized mammalian herbivore.
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Affiliation(s)
- Robert Greenhalgh
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Dylan M Klure
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Teri J Orr
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Noah M Armstrong
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
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Steinbrenner I, Schultheiss UT, Bächle H, Cheng Y, Behning C, Schmid M, Yeo WJ, Yu B, Grams ME, Schlosser P, Stockmann H, Gronwald W, Oefner PJ, Schaeffner E, Eckardt KU, Köttgen A, Sekula P. Associations of Urine and Plasma Metabolites with Kidney Failure and Death in a CKD Cohort. Am J Kidney Dis 2024:S0272-6386(24)00787-X. [PMID: 38815646 DOI: 10.1053/j.ajkd.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 06/01/2024]
Abstract
RATIONALE & OBJECTIVE Biomarkers that enable better identification of persons with chronic kidney disease (CKD) who are at higher risk for disease progression and adverse events are needed. This study sought to identify urine and plasma metabolites associated with progression of kidney disease. STUDY DESIGN Prospective metabolome-wide association study. SETTING & PARTICIPANTS Persons with CKD enrolled in the German CKD Study (GCKD) with metabolite measurements; with external validation within the Atherosclerosis Risk in Communities Study. EXPOSURES 1,513 urine and 1,416 plasma metabolites (Metabolon, Inc.) measured at study entry using untargeted mass spectrometry. OUTCOMES Main endpoints were kidney failure (KF), and a composite endpoint of KF, eGFR <15 mL/min/1.73m2, or 40% decline in eGFR (CKE). Death from any cause was a secondary endpoint. After a median of 6.5 years follow-up, 500 persons experienced KF, 1,083 experienced CKE and 680 died. ANALYTICAL APPROACH Time-to-event analyses using multivariable proportional hazard regression models in a discovery-replication design, with external validation. RESULTS 5,088 GCKD participants were included in analyses of urine metabolites and 5,144 in analyses of plasma metabolites. Among 182 unique metabolites, 30 were significantly associated with KF, 49 with CKE, and 163 with death. The strongest association with KF was observed for plasma hydroxyasparagine (hazard ratio: 1.95, 95% confidence interval: 1.68-2.25). An unnamed metabolite measured in plasma and urine was significantly associated with KF, CKE, and death. External validation of the identified associations of metabolites with KF or CKE revealed direction-consistency for 88% of observed associations. Selected associations of 18 metabolites with study outcomes have not been previously reported. LIMITATIONS Use of observational data and semi-quantitative metabolite measurements at a single time point. CONCLUSIONS The observed associations between metabolites and KF, CKE or death in persons with CKD confirmed previously reported findings and also revealed several associations not previously described. These findings warrant confirmatory research in other study cohorts.
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Affiliation(s)
- Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany
| | - Helena Bächle
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Neurology and Neurophysiology, Faculty of Medicine and Medical Center - University of Freiburg, Breisacher Str. 64, 79106 Freiburg, Germany
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany
| | - Charlotte Behning
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Matthias Schmid
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Wan-Jin Yeo
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Bing Yu
- Department of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Morgan E Grams
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, NY 10016, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Helena Stockmann
- 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, Charitéplatz 1, 10117 Berlin, Germany; Department of Nephrology, University Medical Center Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg
| | - Elke Schaeffner
- Institute of Public Health, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Centre - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany.
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Lu T, Chen Y, Yoshiji S, Ilboudo Y, Forgetta V, Zhou S, Greenwood CMT. Circulating Metabolite Abundances Associated With Risks of Bipolar Disorder, Schizophrenia, and Depression: A Mendelian Randomization Study. Biol Psychiatry 2024:S0006-3223(24)01285-X. [PMID: 38705554 DOI: 10.1016/j.biopsych.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Preventive measures and treatments for psychiatric disorders are limited. Circulating metabolites are potential candidates for biomarker and therapeutic target identification, given their measurability and essential roles in biological processes. METHODS Leveraging large-scale genome-wide association studies, we conducted Mendelian randomization analyses to assess the associations between circulating metabolite abundances and the risks of bipolar disorder, schizophrenia, and depression. Genetic instruments were selected for 94 metabolites measured in the Canadian Longitudinal Study on Aging cohort (N = 8299). We repeated Mendelian randomization analyses based on the UK Biobank, INTERVAL, and EPIC (European Prospective Investigation into Cancer)-Norfolk studies. RESULTS After validating Mendelian randomization assumptions and colocalization evidence, we found that a 1 SD increase in genetically predicted circulating abundances of eicosapentaenoate and docosapentaenoate was associated with odds ratios of 0.72 (95% CI, 0.65-0.79) and 0.63 (95% CI, 0.55-0.72), respectively, for bipolar disorder. Genetically increased Ω-3 unsaturated fatty acids abundance and Ω-3-to-total fatty acids ratio, as well as genetically decreased Ω-6-to-Ω-3 ratio, were negatively associated with the risk of bipolar disorder in the UK Biobank. Genetically increased circulating abundances of 3 N-acetyl-amino acids were associated with an increased risk of schizophrenia with a maximum odds ratio of 1.31 (95% CI, 1.18-1.44) per 1 SD increase. Furthermore, a 1 SD increase in genetically predicted circulating abundance of hypotaurine was associated with an odds ratio of 0.85 (95% CI, 0.78-0.93) for depression. CONCLUSIONS The biological mechanisms that underlie Ω-3 unsaturated fatty acids, NAT8-catalyzed N-acetyl-amino acids, and hypotaurine warrant exploration to identify new biomarkers and potential therapeutic targets.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada.
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Five Prime Sciences Inc., Montréal, Québec, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada; Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Japan Society for the Promotion of Science, Tokyo, Japan
| | - Yann Ilboudo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | | | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, Québec, Canada; McGill Genome Centre, McGill University, Montréal, Québec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada.
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Patel W, Shankar RG, Smith MA, Snodgrass HR, Pirmohamed M, Jorgensen AL, Alfirevic A, Dickens D. Role of Transporters and Enzymes in Metabolism and Distribution of 4-Chlorokynurenine (AV-101). Mol Pharm 2024; 21:550-563. [PMID: 38261609 PMCID: PMC10848289 DOI: 10.1021/acs.molpharmaceut.3c00700] [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: 08/07/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/25/2024]
Abstract
4-Chlorokynurenine (4-Cl-KYN, AV-101) is a prodrug of a NMDA receptor antagonist and is in clinical development for potential CNS indications. We sought to further understand the distribution and metabolism of 4-Cl-KYN, as this information might provide a strategy to enhance the clinical development of this drug. We used excretion studies in rats, in vitro transporter assays, and pharmacogenetic analysis of clinical trial data to determine how 4-Cl-KYN and metabolites are distributed. Our data indicated that a novel acetylated metabolite (N-acetyl-4-Cl-KYN) did not affect the uptake of 4-Cl-KYN across the blood-brain barrier via LAT1. 4-Cl-KYN and its metabolites were found to be renally excreted in rodents. In addition, we found that N-acetyl-4-Cl-KYN inhibited renal and hepatic transporters involved in excretion. Thus, this metabolite has the potential to limit the excretion of a range of compounds. Our pharmacogenetic analysis found that a SNP in N-acetyltransferase 8 (NAT8, rs13538) was linked to levels of N-acetyl-4-Cl-KYN relative to 4-Cl-KYN found in the plasma and that a SNP in SLC7A5 (rs28582913) was associated with the plasma levels of the active metabolite, 7-Cl-KYNA. Thus, we have a pharmacogenetics-based association for plasma drug level that could aid in the drug development of 4-Cl-KYN and have investigated the interaction of a novel metabolite with drug transporters.
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Affiliation(s)
- Waseema Patel
- Department
of Pharmacology and Therapeutics, University
of Liverpool, Liverpool L69 3GL, United
Kingdom
| | - Ravi G. Shankar
- Institute
of Population Health, University of Liverpool, Liverpool L69 3GL, United Kingdom
| | - Mark A. Smith
- Vistagen
Therapeutics, Inc., 343 Allerton Ave, South San Francisco, California 94080, United States
- Medical
College of Georgia, 1120
15th St, Augusta, Georgia 30912, United States
| | - H. Ralph Snodgrass
- Formerly
at Vistagen Therapeutics, Inc., 343 Allerton Ave, South San Francisco, California 94080, United States
| | - Munir Pirmohamed
- Department
of Pharmacology and Therapeutics, University
of Liverpool, Liverpool L69 3GL, United
Kingdom
| | - Andrea L. Jorgensen
- Institute
of Population Health, University of Liverpool, Liverpool L69 3GL, United Kingdom
| | - Ana Alfirevic
- Department
of Pharmacology and Therapeutics, University
of Liverpool, Liverpool L69 3GL, United
Kingdom
| | - David Dickens
- Department
of Pharmacology and Therapeutics, University
of Liverpool, Liverpool L69 3GL, United
Kingdom
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Lu H, Zhang H, Wu Z, Li L. Microbiota-gut-liver-brain axis and hepatic encephalopathy. MICROBIOME RESEARCH REPORTS 2024; 3:17. [PMID: 38841407 PMCID: PMC11149093 DOI: 10.20517/mrr.2023.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 06/07/2024]
Abstract
Hepatic encephalopathy (HE) is a clinical manifestation of neurological and psychiatric abnormalities that are caused by complications of liver dysfunction including hyperammonemia, hyperuricemia, and portal hypertension. Accumulating evidence suggests that HE could be reversed through therapeutic modifications of gut microbiota. Multiple preclinical and clinical studies have indicated that gut microbiome affects the physiological function of the liver, such as the regulation of metabolism, secretion, and immunity, through the gut-liver crosstalk. In addition, gut microbiota also influences the brain through the gut-brain crosstalk, altering its physiological functions including the regulation of the immune, neuroendocrine, and vagal pathways. Thus, key molecules that are involved in the microbiota-gut-liver-brain axis might be able to serve as clinical biomarkers for early diagnosis of HE, and could be effective therapeutic targets for clinical interventions. In this review, we summarize the pathophysiology of HE and further propose approaches modulating the microbiota-gut-liver-brain axis in order to provide a comprehensive understanding of the prevention and potential clinical treatment for HE with a microbiota-targeted therapy.
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Affiliation(s)
| | | | | | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China
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Yin Y, Shan C, Han Q, Chen C, Wang Z, Huang Z, Chen H, Sun L, Fei S, Tao J, Han Z, Tan R, Gu M, Ju X. Causal effects of human serum metabolites on occurrence and progress indicators of chronic kidney disease: a two-sample Mendelian randomization study. Front Nutr 2024; 10:1274078. [PMID: 38260086 PMCID: PMC10800733 DOI: 10.3389/fnut.2023.1274078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Background Chronic kidney disease (CKD) is often accompanied by alterations in the metabolic profile of the body, yet the causative role of these metabolic changes in the onset of CKD remains a subject of ongoing debate. This study investigates the causative links between metabolites and CKD by leveraging the results of genomewide association study (GWAS) from 486 blood metabolites, employing bulk two-sample Mendelian randomization (MR) analyses. Building on the metabolites that exhibit a causal relationship with CKD, we delve deeper using enrichment analysis to identify the metabolic pathways that may contribute to the development and progression of CKD. Methods In conducting the Mendelian randomization analysis, we treated the GWAS data for 486 metabolic traits as exposure variables while using GWAS data for estimated glomerular filtration rate based on serum creatinine (eGFRcrea), microalbuminuria, and the urinary albumin-to-creatinine ratio (UACR) sourced from the CKDGen consortium as the outcome variables. Inverse-variance weighting (IVW) analysis was used to identify metabolites with a causal relationship to outcome. Using Bonferroni correction, metabolites with more robust causal relationships are screened. Additionally, the IVW-positive results were supplemented with the weighted median, MR-Egger, weighted mode, and simple mode. Furthermore, we performed sensitivity analyses using the Cochran Q test, MR-Egger intercept test, MR-PRESSO, and leave-one-out (LOO) test. Pathway enrichment analysis was conducted using two databases, KEGG and SMPDB, for eligible metabolites. Results During the batch Mendelian randomization (MR) analyses, upon completion of the inverse-variance weighted (IVW) approach, sensitivity analysis, and directional consistency checks, 78 metabolites were found to meet the criteria. The following four metabolites satisfy Bonferroni correction: mannose, N-acetylornithine, glycine, and bilirubin (Z, Z), and mannose is causally related to all outcomes of CKD. By pathway enrichment analysis, we identified eight metabolic pathways that contribute to CKD occurrence and progression. Conclusion Based on the present analysis, mannose met Bonferroni correction and had causal associations with CKD, eGFRcrea, microalbuminuria, and UACR. As a potential target for CKD diagnosis and treatment, mannose is believed to play an important role in the occurrence and development of CKD.
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Affiliation(s)
- Yu Yin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Conghui Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianguang Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Congcong Chen
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengkai Huang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Gu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaobing Ju
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Serrano-Marín J, Marin S, Bernal-Casas D, Lillo A, González-Subías M, Navarro G, Cascante M, Sánchez-Navés J, Franco R. A metabolomics study in aqueous humor discloses altered arginine metabolism in Parkinson's disease. Fluids Barriers CNS 2023; 20:90. [PMID: 38049870 PMCID: PMC10696737 DOI: 10.1186/s12987-023-00494-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The lack of accessible and informative biomarkers results in a delayed diagnosis of Parkinson's disease (PD), whose symptoms appear when a significant number of dopaminergic neurons have already disappeared. The retina, a historically overlooked part of the central nervous system (CNS), has gained recent attention. It has been discovered that the composition of cerebrospinal fluid influences the aqueous humor composition through microfluidic circulation. In addition, alterations found in the brain of patients with PD have a correlate in the retina. This new paradigm highlights the potential of the aqueous humor as a sample for identifying differentially concentrated metabolites that could, eventually, become biomarkers if also found altered in blood or CSF of patients. In this research we aim at analyzing the composition of the aqueous humor from healthy controls and PD patients. METHODS A targeted metabolomics approach with concentration determination by mass spectrometry was used. Statistical methods including principal component analysis and linear discriminants were used to select differentially concentrated metabolites that allow distinguishing patients from controls. RESULTS In this first metabolomics study in the aqueous humor of PD patients, elevated levels of 16 compounds were found; molecules differentially concentrated grouped into biogenic amines, amino acids, and acylcarnitines. A biogenic amine, putrescine, alone could be a metabolite capable of differentiating between PD and control samples. The altered levels of the metabolites were correlated, suggesting that the elevations stem from a common mechanism involving arginine metabolism. CONCLUSIONS A combination of three metabolites, putrescine, tyrosine, and carnitine was able to correctly classify healthy participants from PD patients. Altered metabolite levels suggest altered arginine metabolism. The pattern of metabolomic disturbances was not due to the levodopa-based dopamine replacement medication because one of the patients was not yet taking levodopa but a dopamine receptor agonist.
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Affiliation(s)
- Joan Serrano-Marín
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, 08028, Spain
- CIBEREHD. Network Center for Hepatic and Digestive Diseases, National Spanish Health Institute Carlos III (ISCIII), Madrid, 28029, Spain
| | - David Bernal-Casas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, 08028, Spain
| | - Alejandro Lillo
- Department of Biochemistry and Physiology, Universitat de Barcelona, Barcelona, Spain
| | - Marc González-Subías
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Navarro
- Department of Biochemistry and Physiology, Universitat de Barcelona, Barcelona, Spain
- CiberNed. Network Center for Biomedical Research in Neurodegenerative Diseases., Spanish National Health Institute Carlos iii, Av. Monforte de Lemos, 3-5, Madrid, 28029, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, 08028, Spain
- CIBEREHD. Network Center for Hepatic and Digestive Diseases, National Spanish Health Institute Carlos III (ISCIII), Madrid, 28029, Spain
| | - Juan Sánchez-Navés
- Department of Ophthalmology, Ophthalmedic and I.P.O. Institute of Ophthalmology, Palma de Mallorca, Spain
| | - Rafael Franco
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain.
- CiberNed. Network Center for Biomedical Research in Neurodegenerative Diseases., Spanish National Health Institute Carlos iii, Av. Monforte de Lemos, 3-5, Madrid, 28029, Spain.
- School of Chemistry, Universitat de Barcelona, Barcelona, Spain.
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9
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Georgiou-Siafis SK, Tsiftsoglou AS. The Key Role of GSH in Keeping the Redox Balance in Mammalian Cells: Mechanisms and Significance of GSH in Detoxification via Formation of Conjugates. Antioxidants (Basel) 2023; 12:1953. [PMID: 38001806 PMCID: PMC10669396 DOI: 10.3390/antiox12111953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Glutathione (GSH) is a ubiquitous tripeptide that is biosynthesized in situ at high concentrations (1-5 mM) and involved in the regulation of cellular homeostasis via multiple mechanisms. The main known action of GSH is its antioxidant capacity, which aids in maintaining the redox cycle of cells. To this end, GSH peroxidases contribute to the scavenging of various forms of ROS and RNS. A generally underestimated mechanism of action of GSH is its direct nucleophilic interaction with electrophilic compounds yielding thioether GSH S-conjugates. Many compounds, including xenobiotics (such as NAPQI, simvastatin, cisplatin, and barbital) and intrinsic compounds (such as menadione, leukotrienes, prostaglandins, and dopamine), form covalent adducts with GSH leading mainly to their detoxification. In the present article, we wish to present the key role and significance of GSH in cellular redox biology. This includes an update on the formation of GSH-S conjugates or GSH adducts with emphasis given to the mechanism of reaction, the dependence on GST (GSH S-transferase), where this conjugation occurs in tissues, and its significance. The uncovering of the GSH adducts' formation enhances our knowledge of the human metabolome. GSH-hematin adducts were recently shown to have been formed spontaneously in multiples isomers at hemolysates, leading to structural destabilization of the endogenous toxin, hematin (free heme), which is derived from the released hemoglobin. Moreover, hemin (the form of oxidized heme) has been found to act through the Kelch-like ECH associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor-2 (Nrf2) signaling pathway as an epigenetic modulator of GSH metabolism. Last but not least, the implications of the genetic defects in GSH metabolism, recorded in hemolytic syndromes, cancer and other pathologies, are presented and discussed under the framework of conceptualizing that GSH S-conjugates could be regarded as signatures of the cellular metabolism in the diseased state.
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Affiliation(s)
| | - Asterios S. Tsiftsoglou
- Laboratory of Pharmacology, Department of Pharmaceutical Sciences, School of Health Sciences, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece;
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10
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Lee AM, Xu Y, Hooper SR, Abraham AG, Hu J, Xiao R, Matheson MB, Brunson C, Rhee EP, Coresh J, Vasan RS, Schrauben S, Kimmel PL, Warady BA, Furth SL, Hartung EA, Denburg MR. Circulating Metabolomic Associations with Neurocognitive Outcomes in Pediatric CKD. Clin J Am Soc Nephrol 2023; 19:01277230-990000000-00269. [PMID: 37871960 PMCID: PMC10843217 DOI: 10.2215/cjn.0000000000000318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Children with CKD are at risk for impaired neurocognitive functioning. We investigated metabolomic associations with neurocognition in children with CKD. METHODS We leveraged data from the Chronic Kidney Disease in Children (CKiD) study and the Neurocognitive Assessment and Magnetic Resonance Imaging Analysis of Children and Young Adults with Chronic Kidney Disease (NiCK) study. CKiD is a multi-institutional cohort that enrolled children aged 6 months to 16 years with eGFR 30-90 ml/min per 1.73 m 2 ( n =569). NiCK is a single-center cross-sectional study of participants aged 8-25 years with eGFR<90 ml/min per 1.73 m 2 ( n =60) and matched healthy controls ( n =67). Untargeted metabolomic quantification was performed on plasma (CKiD, 622 metabolites) and serum (NiCK, 825 metabolites) samples. Four neurocognitive domains were assessed: intelligence, attention regulation, working memory, and parent ratings of executive function. Repeat assessments were performed in CKiD at 2-year intervals. Linear regression and linear mixed-effects regression analyses adjusting for age, sex, delivery history, hypertension, proteinuria, CKD duration, and glomerular versus nonglomerular diagnosis were used to identify metabolites associated with neurocognitive z-scores. Analyses were performed with and without adjustment for eGFR. RESULTS There were multiple metabolite associations with neurocognition observed in at least two of the analytic samples (CKiD baseline, CKiD follow-up, and NiCK CKD). Most of these metabolites were significantly elevated in children with CKD compared with healthy controls in NiCK. Notable signals included associations with parental ratings of executive function: phenylacetylglutamine, indoleacetylglutamine, and trimethylamine N-oxide-and with intelligence: γ -glutamyl amino acids and aconitate. CONCLUSIONS Several metabolites were associated with neurocognitive dysfunction in pediatric CKD, implicating gut microbiome-derived substances, mitochondrial dysfunction, and altered energy metabolism, circulating toxins, and redox homeostasis.
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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
| | - Stephen R. Hooper
- Department of Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina
| | - Alison G. Abraham
- Department of Epidemiology, Colorado University School of Public Health, Aurora, Colorado
| | - 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
| | - Matthew B. Matheson
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Celina Brunson
- Division of Nephrology, Children's National Hospital, Washington, DC
| | - Eugene P. Rhee
- Division of Nephrology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard School of Medicine, Boston, Massachusetts
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ramachandran S. Vasan
- Boston University School of Medicine, Boston, Massachusetts
- Boston University School of Public Health, Boston, Massachusetts
| | - Sarah Schrauben
- Perelman School of Medicine at the University of Pennsylvania, Department of Medicine and Department of Biostatistics, Epidemiology, and Informatics, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - 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
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Department of Pediatrics and Department of Biostatistics, Epidemiology, and Informatics, Philadelphia, Pennsylvania
| | - Erum A. Hartung
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michelle R. Denburg
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Department of Pediatrics and Department of Biostatistics, Epidemiology, and Informatics, Philadelphia, Pennsylvania
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11
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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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12
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Lillo A, Marin S, Serrano-Marín J, Bernal-Casas D, Binetti N, Navarro G, Cascante M, Sánchez-Navés J, Franco R. Biogenic Amine Levels Markedly Increase in the Aqueous Humor of Individuals with Controlled Type 2 Diabetes. Int J Mol Sci 2022; 23:ijms232112752. [PMID: 36361545 PMCID: PMC9658658 DOI: 10.3390/ijms232112752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The composition of the aqueous humor of patients with type 2 diabetes is relevant to understanding the underlying causes of eye-related comorbidities. Information on the composition of aqueous humor in healthy subjects is limited due to the lack of adequate controls. To carry out a metabolomics study, 31 samples of aqueous humor from healthy subjects without ocular pathology, submitted to refractive surgery and seven samples from patients with type 2 diabetes without signs of ocular pathology related to diabetes were used. The level of 25 molecules was significantly (p < 0.001) altered in the aqueous humor of the patient group. The concentration of a single molecule, N-acetylornithine, makes it possible to discriminate between control and diabetes (sensitivity and specificity equal to 1). In addition, receptor operating characteristic curve and principal component analysis for the above-mentioned six molecules yielded significantly (p < 0.001) altered in the aqueous humor of the patient group. In addition, receptor operating characteristic curve and principal component analysis for six compounds yielded cut-off values and remarkable sensitivity, specificity, and segregation ability. The altered level of N-acetylornithine may be due to an increased amount of acetate in diabetes. It is of interest to further investigate whether this alteration is related to the pathogenesis of the disease. The increase in the amino form of pyruvate, alanine, in diabetes is also relevant because it could be a means of reducing the formation of lactate from pyruvate.
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Affiliation(s)
- Alejandro Lillo
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08028 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
- CIBEREHD, Network Center for Hepatic and Digestive Diseases, National Spanish Health Institute Carlos III (ISCIII), 28029 Madrid, Spain
| | - Joan Serrano-Marín
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - David Bernal-Casas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Nicolas Binetti
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gemma Navarro
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08028 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
- CIBEREHD, Network Center for Hepatic and Digestive Diseases, National Spanish Health Institute Carlos III (ISCIII), 28029 Madrid, Spain
| | - Juan Sánchez-Navés
- Department of Ophthalmology, Ophthalmedic and I.P.O, Institute of Ophthalmology, 07011 Palma de Mallorca, Spain
| | - Rafael Franco
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08028 Barcelona, Spain
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
- School of Chemistry, Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence:
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13
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Correia MJ, Pimpão AB, Fernandes DGF, Morello J, Sequeira CO, Calado J, Antunes AMM, Almeida MS, Branco P, Monteiro EC, Vicente JB, Serpa J, Pereira SA. Cysteine as a Multifaceted Player in Kidney, the Cysteine-Related Thiolome and Its Implications for Precision Medicine. Molecules 2022; 27:1416. [PMID: 35209204 PMCID: PMC8874463 DOI: 10.3390/molecules27041416] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
In this review encouraged by original data, we first provided in vivo evidence that the kidney, comparative to the liver or brain, is an organ particularly rich in cysteine. In the kidney, the total availability of cysteine was higher in cortex tissue than in the medulla and distributed in free reduced, free oxidized and protein-bound fractions (in descending order). Next, we provided a comprehensive integrated review on the evidence that supports the reliance on cysteine of the kidney beyond cysteine antioxidant properties, highlighting the relevance of cysteine and its renal metabolism in the control of cysteine excess in the body as a pivotal source of metabolites to kidney biomass and bioenergetics and a promoter of adaptive responses to stressors. This view might translate into novel perspectives on the mechanisms of kidney function and blood pressure regulation and on clinical implications of the cysteine-related thiolome as a tool in precision medicine.
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Affiliation(s)
- Maria João Correia
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - António B. Pimpão
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - Dalila G. F. Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), 2780-157 Oeiras, Portugal; (D.G.F.F.); (J.B.V.)
| | - Judit Morello
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - Catarina O. Sequeira
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - Joaquim Calado
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal;
- Nephrology Department, Centro Hospitalar Universitário de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Alexandra M. M. Antunes
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, 1049-001 Lisboa, Portugal;
| | - Manuel S. Almeida
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
- Hospital de Santa Cruz, Centro Hospitalar de Lisboa Ocidental, 2790-134 Carnaxide, Portugal
| | - Patrícia Branco
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
- Hospital de Santa Cruz, Centro Hospitalar de Lisboa Ocidental, 2790-134 Carnaxide, Portugal
| | - Emília C. Monteiro
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), 2780-157 Oeiras, Portugal; (D.G.F.F.); (J.B.V.)
| | - Jacinta Serpa
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), 1099-023 Lisboa, Portugal
| | - Sofia A. Pereira
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
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14
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N-Acetyltransferase 8 Promotes Viral Replication by Increasing the Stability of Enterovirus 71 Nonstructural Proteins. J Virol 2022; 96:e0011922. [PMID: 35170979 PMCID: PMC8941898 DOI: 10.1128/jvi.00119-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterovirus 71 (EV71) is deemed as a re-emergent pathogen with recent outbreaks worldwide. EV71 infection causes hand, foot and mouth disease (HFMD) and has been associated with severe cardiac and central nervous system complications and even death. Viruses need host factors to complete their life cycle, thus the identification of the host factors for EV71 infection is pivotal to new antiviral research. Emerging evidence has highlighted the importance of protein acetylation during infection of various human viruses. The endoplasmic reticulum, as the prominent organelle of EV71 replication, also has its unique acetylation regulation mechanism. However, the pathogenesis of EV71 and its relationship with the ER-based acetylation machinery are not fully understood. In this study, we demonstrated for the first time that the ER-resident acetyltransferase NAT8 is a host factor for EV71 infection. Inhibiting NAT8 with CRISPR or a small compound significantly suppressed EV71 infection in SK-N-SH cells. NAT8 promoted EV71 replication in an acetyltransferase activity-dependent manner. Additionally, we found NAT8 facilitates EV71 infection through interacting with EV71 2B,3AB and 3C proteins and increasing the stability of these proteins. These results uncovered a novel function of NAT8 and elucidated a new mechanism underlying the regulation of EV71 replication. Importance Enterovirus 71 (EV71) is one of the most common pathogens that cause hand, foot and mouth disease in young children and some patients experience severe or fatal neurologic consequences. To ensure efficient replication, the virus must hijack multiple host factors for its own benefit. Here we show that the ER-resident acetyltransferase NAT8 is a host factor for EV71 infection. EV71 fails to complete its infection in various cells in the absence of NAT8. We further show that NAT8 benefits EV71 replication in an acetyltransferase activity-dependent manner. Finally, we show that NAT8 facilitates EV71 infection through interacting with EV71 2B,3AB and 3C proteins and increasing the stability of these proteins. These results uncovered a novel function of NAT8 in EV71 infection and elucidated a new mechanism underlying the regulation of EV71 replication.
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15
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Jiang H, Tang E, Chen Y, Liu H, Zhao Y, Lin M, He L. FDFT1 predicts poor prognosis in stage I-III colon adenocarcinoma and synergizes SQLE to promote tumor progression. Cancer Sci 2021; 113:971-985. [PMID: 34939274 PMCID: PMC8898704 DOI: 10.1111/cas.15248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022] Open
Abstract
Colon adenocarcinoma (COAD) is one of the most prevalent malignancies, with poor prognosis and lack of effective treatment targets. Squalene synthase (FDFT1) is an upstream enzyme of squalene epoxidase (SQLE) in cholesterol biosynthesis. In a previous study, we revealed that SQLE promotes colon cancer cell proliferation in vitro and in vivo. Here, we investigate the prognostic value of FDFT1 in stage I‐III COAD and explore the potential underlying mechanisms. Squalene synthase was significantly upregulated in stage I‐III COAD and positively correlated with poor differentiation and advanced tumor stage. High expression of FDFT1 was an independent predictor of overall and relapse‐free survival, and the nomograms based on FDFT1 could effectively identify patients at high risk of poor outcome. Squalene synthase accelerated colon cancer cell proliferation and promoted tumor growth. Lack of FDFT1 resulted in accumulating NAT8 and D‐pantethine to lower reactive oxygen species levels and inhibit colon cancer cell proliferation. Moreover, the combined inhibition of FDFT1 and SQLE induced a greater suppressive effect on cell proliferation and tumor growth than single inhibition. Taken together, these results indicate that FDFT1 predicts poor prognosis in stage I‐III COAD and has the tumor‐promoting effect on COAD through regulating NAT8 and D‐pantethine. Targeting both FDFT1 and SQLE is a more promising therapy than their single inhibition for stage I‐III COAD.
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Affiliation(s)
- Huihong Jiang
- Department of General Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China.,Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Erjiang Tang
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, 200090, China.,Center for clinical research and translational medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Ying Chen
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, 200090, China.,Center for clinical research and translational medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Hailong Liu
- Department of General Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China.,Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Yun Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,The State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Moubin Lin
- Department of General Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China.,Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, 200090, China.,Center for clinical research and translational medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Luwei He
- Institute of Gastrointestinal Surgery and Translational Medicine, School of Medicine, Tongji University, Shanghai, 200090, China.,Center for clinical research and translational medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
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16
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Anuntakarun S, Larbcharoensub N, Payungporn S, Reamtong O. Identification of genes associated with Kikuchi-Fujimoto disease using RNA and exome sequencing. Mol Cell Probes 2021; 57:101728. [PMID: 33819568 DOI: 10.1016/j.mcp.2021.101728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 12/15/2022]
Abstract
Kikuchi-Fujimoto disease (KFD) is an extremely rare disease, and although it is reported to have a worldwide distribution, young Asian women are most likely to be affected. Although this disease is generally benign and self-limiting, distinguishing it from other diseases that cause lymphadenopathy (e.g., leukemia, lymphoma, and infectious diseases) is challenging. A lymph node biopsy is a definitive diagnostic technique for KFD and only requires skillful pathologists. There are no specific symptoms or laboratory tests for KFD, and more than 50% of KFD patients have suffered from being misdiagnosed with lymphoma, which leads to improper treatment. In this study, lymph node tissue samples from KFD patients were used to reveal their exomes and transcriptomes using a high-throughput nucleotide sequencer. Fourteen single nucleotide polymorphisms (SNPs) were identified as candidate KFD markers and were compared with a healthy lymph node exome dataset. The mutation of these genes caused disruptive impact in the proteins. Several SNPs associated with KFD involve genes related to human cancers, olfaction, and osteoblast differentiation. According to the transcriptome data, there were 238 up-regulated and 1,519 down-regulated genes. RANBP2-like and ribosomal protein L13 were the most up-regulated and down-regulated genes in KFD patients, respectively. The altered gene expression involved in the human immune system, chromatin remodeling, and gene transcription. A comparison of KFD and healthy datasets of exomes and transcriptomes may allow further insights into the KFD phenotype. The results may also facilitate future KFD diagnosis and treatment.
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Affiliation(s)
- Songtham Anuntakarun
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Noppadol Larbcharoensub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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17
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Gonçalves-Dias C, Sequeira CO, Vicente JB, Correia MJ, Coelho NR, Morello J, Antunes AMM, Soto K, Monteiro EC, Pereira SA. A Mechanistic-Based and Non-invasive Approach to Quantify the Capability of Kidney to Detoxify Cysteine-Disulfides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1306:109-120. [PMID: 33959909 DOI: 10.1007/978-3-030-63908-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Our general goal was to non-invasively evaluate kidney tubular dysfunction. We developed a strategy based on cysteine (Cys) disulfide stress mechanism that underlies kidney dysfunction. There is scarce information regarding the fate of Cys-disulfides (CysSSX), but evidence shows they might be detoxified in proximal tubular cells by the action of N-acetyltransferase 8 (NAT8). This enzyme promotes the addition of an N-acetyl moiety to cysteine-S-conjugates, forming mercapturates that are eliminated in urine. Therefore, we developed a strategy to quantify mercapturates of CysSSX in urine as surrogate of disulfide stress and NAT8 activity in kidney tubular cells. We use a reduction agent for the selective reduction of disulfide bonds. The obtained N-acetylcysteine moiety of the mercapturates from cysteine disulfides was monitored by fluorescence detection. The method was applied to urine from mice and rat as well as individuals with healthy kidney and kidney disease.
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Affiliation(s)
- Clara Gonçalves-Dias
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Catarina O Sequeira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - M João Correia
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Nuno R Coelho
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Judit Morello
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Alexandra M M Antunes
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Karina Soto
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal.,Hospital Prof. Dr. Fernando da Fonseca, EPE, Amadora, Portugal
| | - Emília C Monteiro
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Sofia A Pereira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal.
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18
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Rigby MJ, Lawton AJ, Kaur G, Banduseela VC, Kamm WE, Lakkaraju A, Denu JM, Puglielli L. Endoplasmic reticulum acetyltransferases Atase1 and Atase2 differentially regulate reticulophagy, macroautophagy and cellular acetyl-CoA metabolism. Commun Biol 2021; 4:454. [PMID: 33846551 PMCID: PMC8041774 DOI: 10.1038/s42003-021-01992-8] [Citation(s) in RCA: 3] [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: 10/27/2020] [Accepted: 03/17/2021] [Indexed: 12/25/2022] Open
Abstract
Nε-lysine acetylation in the ER lumen is a recently discovered quality control mechanism that ensures proteostasis within the secretory pathway. The acetyltransferase reaction is carried out by two type-II membrane proteins, ATase1/NAT8B and ATase2/NAT8. Prior studies have shown that reducing ER acetylation can induce reticulophagy, increase ER turnover, and alleviate proteotoxic states. Here, we report the generation of Atase1-/- and Atase2-/- mice and show that these two ER-based acetyltransferases play different roles in the regulation of reticulophagy and macroautophagy. Importantly, knockout of Atase1 alone results in activation of reticulophagy and rescue of the proteotoxic state associated with Alzheimer's disease. Furthermore, loss of Atase1 or Atase2 results in widespread adaptive changes in the cell acetylome and acetyl-CoA metabolism. Overall, our study supports a divergent role of Atase1 and Atase2 in cellular biology, emphasizing ATase1 as a valid translational target for diseases characterized by toxic protein aggregation in the secretory pathway.
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Affiliation(s)
- Michael J Rigby
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexis J Lawton
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Gulpreet Kaur
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Varuna C Banduseela
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - William E Kamm
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Aparna Lakkaraju
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Ophthalmology and Anatomy, University of California, San Francisco, CA, USA
| | - John M Denu
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA.
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, USA.
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19
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Steinbrenner I, Schultheiss UT, Kotsis F, Schlosser P, Stockmann H, Mohney RP, Schmid M, Oefner PJ, Eckardt KU, Köttgen A, Sekula P. Urine Metabolite Levels, Adverse Kidney Outcomes, and Mortality in CKD Patients: A Metabolome-wide Association Study. Am J Kidney Dis 2021; 78:669-677.e1. [PMID: 33839201 DOI: 10.1053/j.ajkd.2021.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/22/2021] [Indexed: 01/01/2023]
Abstract
RATIONALE & OBJECTIVE Mechanisms underlying the variable course of disease progression in patients with chronic kidney disease (CKD) are incompletely understood. The aim of this study was to identify novel biomarkers of adverse kidney outcomes and overall mortality, which may offer insights into pathophysiologic mechanisms. STUDY DESIGN Metabolome-wide association study. SETTING & PARTICIPANTS 5,087 patients with CKD enrolled in the observational German Chronic Kidney Disease Study. EXPOSURES Measurements of 1,487 metabolites in urine. OUTCOMES End points of interest were time to kidney failure (KF), a combined end point of KF and acute kidney injury (KF+AKI), and overall mortality. ANALYTICAL APPROACH Statistical analysis was based on a discovery-replication design (ratio 2:1) and multivariable-adjusted Cox regression models. RESULTS After a median follow-up of 4 years, 362 patients died, 241 experienced KF, and 382 experienced KF+AKI. Overall, we identified 55 urine metabolites whose levels were significantly associated with adverse kidney outcomes and/or mortality. Higher levels of C-glycosyltryptophan were consistently associated with all 3 main end points (hazard ratios of 1.43 [95% CI, 1.27-1.61] for KF, 1.40 [95% CI, 1.27-1.55] for KF+AKI, and 1.47 [95% CI, 1.33-1.63] for death). Metabolites belonging to the phosphatidylcholine pathway showed significant enrichment. Members of this pathway contributed to the improvement of the prediction performance for KF observed when multiple metabolites were added to the well-established Kidney Failure Risk Equation. LIMITATIONS Findings among patients of European ancestry with CKD may not be generalizable to the general population. CONCLUSIONS Our comprehensive screen of the association between urine metabolite levels and adverse kidney outcomes and mortality identifies metabolites that predict KF and represents a valuable resource for future studies of biomarkers of CKD progression.
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Affiliation(s)
- Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg; Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg; Department of Medicine IV-Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg
| | - Helena Stockmann
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin
| | | | - Matthias Schmid
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin; Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen; Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg.
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg.
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20
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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] [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
- grid.5963.9Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- grid.5963.9Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Johannes Hertel
- grid.6142.10000 0004 0488 0789School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland ,grid.5603.0University of Greifswald, University Medicine Greifswald, Department of Psychiatry and Psychotherapy, Greifswald, Germany
| | - Peggy Sekula
- grid.5963.9Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Peter J. Oefner
- grid.7727.50000 0001 2190 5763Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Ute Spiekerkoetter
- grid.5963.9Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Johanna Mielke
- grid.420044.60000 0004 0374 4101Bayer AG, Division Pharmaceuticals, Open Innovation & Digital Technologies, Wuppertal, Germany
| | - Daniel F. Freitag
- grid.420044.60000 0004 0374 4101Bayer AG, Division Pharmaceuticals, Open Innovation & Digital Technologies, Wuppertal, Germany
| | - Miriam Schmidts
- grid.5963.9Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | | | - Florian Kronenberg
- grid.5361.10000 0000 8853 2677Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- grid.5330.50000 0001 2107 3311Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany ,grid.6363.00000 0001 2218 4662Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ines Thiele
- grid.6142.10000 0004 0488 0789School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland ,grid.6142.10000 0004 0488 0789Division of Microbiology, National University of Ireland, Galway, University Road, Galway, Ireland ,APC Microbiome Ireland, Galway, Ireland
| | - Yong Li
- grid.5963.9Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- grid.5963.9Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany ,grid.5963.9CIBSS – Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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21
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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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22
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PharmGKB summary: lamotrigine pathway, pharmacokinetics and pharmacodynamics. Pharmacogenet Genomics 2020; 30:81-90. [PMID: 32187155 DOI: 10.1097/fpc.0000000000000397] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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23
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Zhang A, Li CY, Kelly EJ, Sheppard L, Cui JY. Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA- PCG pairs involved in intermediary metabolism. PLoS One 2020; 15:e0224644. [PMID: 32101552 PMCID: PMC7043721 DOI: 10.1371/journal.pone.0224644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Polybrominated diphenyl ethers (PBDEs) were formally used as flame-retardants and are chemically stable, lipophlic persistent organic pollutants which are known to bioaccumulate in humans. Although its toxicities are well characterized, little is known about the changes in transcriptional regulation caused by PBDE exposure. Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of transcriptional and translational processes. It is hypothesized that lncRNAs can regulate nearby protein-coding genes (PCGs) and changes in the transcription of lncRNAs may act in cis to perturb gene expression of its neighboring PCGs. The goals of this study were to 1) characterize PCGs and lncRNAs that are differentially regulated from exposure to PBDEs; 2) identify PCG-lncRNA pairs through genome annotation and predictive binding tools; and 3) determine enriched canonical pathways caused by differentially expressed lncRNA-PCGs pairs. HepaRG cells, which are human-derived hepatic cells that accurately represent gene expression profiles of human liver tissue, were exposed to BDE-47 and BDE-99 at a dose of 25 μM for 24 hours. Differentially expressed lncRNA-PCG pairs were identified through DESeq2 and HOMER; significant canonical pathways were determined through Ingenuity Pathway Analysis (IPA). LncTar was used to predict the binding of 19 lncRNA-PCG pairs with known roles in drug-processing pathways. Genome annotation revealed that the majority of the differentially expressed lncRNAs map to PCG introns. PBDEs regulated overlapping pathways with PXR and CAR such as protein ubiqutination pathway and peroxisome proliferator-activated receptor alpha-retinoid X receptor alpha (PPARα-RXRα) activation but also regulate distinctive pathways involved in intermediary metabolism. PBDEs uniquely down-regulated GDP-L-fucose biosynthesis, suggesting its role in modifying important pathways involved in intermediary metabolism such as carbohydrate and lipid metabolism. In conclusion, we provide strong evidence that PBDEs regulate both PCGs and lncRNAs in a PXR/CAR ligand-dependent and independent manner.
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Affiliation(s)
- Angela Zhang
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States of America
| | - Cindy Yanfei Li
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States of America
| | - Edward J. Kelly
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States of America
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
| | - Lianne Sheppard
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States of America
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24
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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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25
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Abstract
The mercapturic acid pathway is a major route for the biotransformation of xenobiotic and endobiotic electrophilic compounds and their metabolites. Mercapturic acids (N-acetyl-l-cysteine S-conjugates) are formed by the sequential action of the glutathione transferases, γ-glutamyltransferases, dipeptidases, and cysteine S-conjugate N-acetyltransferase to yield glutathione S-conjugates, l-cysteinylglycine S-conjugates, l-cysteine S-conjugates, and mercapturic acids; these metabolites constitute a "mercapturomic" profile. Aminoacylases catalyze the hydrolysis of mercapturic acids to form cysteine S-conjugates. Several renal transport systems facilitate the urinary elimination of mercapturic acids; urinary mercapturic acids may serve as biomarkers for exposure to chemicals. Although mercapturic acid formation and elimination is a detoxication reaction, l-cysteine S-conjugates may undergo bioactivation by cysteine S-conjugate β-lyase. Moreover, some l-cysteine S-conjugates, particularly l-cysteinyl-leukotrienes, exert significant pathophysiological effects. Finally, some enzymes of the mercapturic acid pathway are described as the so-called "moonlighting proteins," catalytic proteins that exert multiple biochemical or biophysical functions apart from catalysis.
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Affiliation(s)
- Patrick E Hanna
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
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26
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Zuhra K, Tomé CS, Masi L, Giardina G, Paulini G, Malagrinò F, Forte E, Vicente JB, Giuffrè A. N-Acetylcysteine Serves as Substrate of 3-Mercaptopyruvate Sulfurtransferase and Stimulates Sulfide Metabolism in Colon Cancer Cells. Cells 2019; 8:cells8080828. [PMID: 31382676 PMCID: PMC6721681 DOI: 10.3390/cells8080828] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/12/2022] Open
Abstract
Hydrogen sulfide (H2S) is an endogenously produced signaling molecule. The enzymes 3-mercaptopyruvate sulfurtransferase (MST), partly localized in mitochondria, and the inner mitochondrial membrane-associated sulfide:quinone oxidoreductase (SQR), besides being respectively involved in the synthesis and catabolism of H2S, generate sulfane sulfur species such as persulfides and polysulfides, currently recognized as mediating some of the H2S biological effects. Reprogramming of H2S metabolism was reported to support cellular proliferation and energy metabolism in cancer cells. As oxidative stress is a cancer hallmark and N-acetylcysteine (NAC) was recently suggested to act as an antioxidant by increasing intracellular levels of sulfane sulfur species, here we evaluated the effect of prolonged exposure to NAC on the H2S metabolism of SW480 colon cancer cells. Cells exposed to NAC for 24 h displayed increased expression and activity of MST and SQR. Furthermore, NAC was shown to: (i) persist at detectable levels inside the cells exposed to the drug for up to 24 h and (ii) sustain H2S synthesis by human MST more effectively than cysteine, as shown working on the isolated recombinant enzyme. We conclude that prolonged exposure of colon cancer cells to NAC stimulates H2S metabolism and that NAC can serve as a substrate for human MST.
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Affiliation(s)
- Karim Zuhra
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Catarina S Tomé
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Avenida da República (EAN), 2780-157 Oeiras, Portugal
| | - Letizia Masi
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giulia Paulini
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Francesca Malagrinò
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy.
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Avenida da República (EAN), 2780-157 Oeiras, Portugal.
| | - Alessandro Giuffrè
- CNR Institute of Molecular Biology and Pathology, Piazzale Aldo Moro 5, I-00185 Rome, Italy.
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27
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The mercapturomic profile of health and non-communicable diseases. High Throughput 2019; 8:ht8020010. [PMID: 31018482 PMCID: PMC6630208 DOI: 10.3390/ht8020010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/17/2022] Open
Abstract
The mercapturate pathway is a unique metabolic circuitry that detoxifies electrophiles upon adducts formation with glutathione. Since its discovery over a century ago, most of the knowledge on the mercapturate pathway has been provided from biomonitoring studies on environmental exposure to toxicants. However, the mercapturate pathway-related metabolites that is formed in humans—the mercapturomic profile—in health and disease is yet to be established. In this paper, we put forward the hypothesis that these metabolites are key pathophysiologic factors behind the onset and development of non-communicable chronic inflammatory diseases. This review goes from the evidence in the formation of endogenous metabolites undergoing the mercapturate pathway to the methodologies for their assessment and their association with cancer and respiratory, neurologic and cardiometabolic diseases.
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28
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Köttgen A, Raffler J, Sekula P, Kastenmüller G. Genome-Wide Association Studies of Metabolite Concentrations (mGWAS): Relevance for Nephrology. Semin Nephrol 2019; 38:151-174. [PMID: 29602398 DOI: 10.1016/j.semnephrol.2018.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metabolites are small molecules that are intermediates or products of metabolism, many of which are freely filtered by the kidneys. In addition, the kidneys have a central role in metabolite anabolism and catabolism, as well as in active metabolite reabsorption and/or secretion during tubular passage. This review article illustrates how the coupling of genomics and metabolomics in genome-wide association analyses of metabolites can be used to illuminate mechanisms underlying human metabolism, with a special focus on insights relevant to nephrology. First, genetic susceptibility loci for reduced kidney function and chronic kidney disease (CKD) were reviewed systematically for their associations with metabolite concentrations in metabolomics studies of blood and urine. Second, kidney function and CKD-associated metabolites reported from observational studies were interrogated for metabolite-associated genetic variants to generate and discuss complementary insights. Finally, insights originating from the simultaneous study of both blood and urine or by modeling intermetabolite relationships are summarized. We also discuss methodologic questions related to the study of metabolite concentrations in urine as well as among CKD patients. In summary, genome-wide association analyses of metabolites using metabolite concentrations quantified from blood and/or urine are a promising avenue of research to illuminate physiological and pathophysiological functions of the kidney.
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Affiliation(s)
- Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
| | - Johannes Raffler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
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29
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Farrugia MA, Puglielli L. Nε-lysine acetylation in the endoplasmic reticulum - a novel cellular mechanism that regulates proteostasis and autophagy. J Cell Sci 2018; 131:131/22/jcs221747. [PMID: 30446507 DOI: 10.1242/jcs.221747] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein post-translational modifications (PTMs) take many shapes, have many effects and are necessary for cellular homeostasis. One of these PTMs, Nε-lysine acetylation, was thought to occur only in the mitochondria, cytosol and nucleus, but this paradigm was challenged in the past decade with the discovery of lysine acetylation in the lumen of the endoplasmic reticulum (ER). This process is governed by the ER acetylation machinery: the cytosol:ER-lumen acetyl-CoA transporter AT-1 (also known as SLC33A1), and the ER-resident lysine acetyltransferases ATase1 and ATase2 (also known as NAT8B and NAT8, respectively). This Review summarizes the more recent biochemical, cellular and mouse model studies that underscore the importance of the ER acetylation process in maintaining protein homeostasis and autophagy within the secretory pathway, and its impact on developmental and age-associated diseases.
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Affiliation(s)
- Mark A Farrugia
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA .,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA.,Geriatric Research Education Clinical Center, VA Medical Center, Madison, WI 53705, USA
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30
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Hebebrand J, Peters T, Schijven D, Hebebrand M, Grasemann C, Winkler TW, Heid IM, Antel J, Föcker M, Tegeler L, Brauner L, Adan RAH, Luykx JJ, Correll CU, König IR, Hinney A, Libuda L. The role of genetic variation of human metabolism for BMI, mental traits and mental disorders. Mol Metab 2018; 12:1-11. [PMID: 29673576 PMCID: PMC6001916 DOI: 10.1016/j.molmet.2018.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE The aim was to assess whether loci associated with metabolic traits also have a significant role in BMI and mental traits/disorders METHODS: We first assessed the number of single nucleotide polymorphisms (SNPs) with genome-wide significance for human metabolism (NHGRI-EBI Catalog). These 516 SNPs (216 independent loci) were looked-up in genome-wide association studies for association with body mass index (BMI) and the mental traits/disorders educational attainment, neuroticism, schizophrenia, well-being, anxiety, depressive symptoms, major depressive disorder, autism-spectrum disorder, attention-deficit/hyperactivity disorder, Alzheimer's disease, bipolar disorder, aggressive behavior, and internalizing problems. A strict significance threshold of p < 6.92 × 10-6 was based on the correction for 516 SNPs and all 14 phenotypes, a second less conservative threshold (p < 9.69 × 10-5) on the correction for the 516 SNPs only. RESULTS 19 SNPs located in nine independent loci revealed p-values < 6.92 × 10-6; the less strict criterion was met by 41 SNPs in 24 independent loci. BMI and schizophrenia showed the most pronounced genetic overlap with human metabolism with three loci each meeting the strict significance threshold. Overall, genetic variation associated with estimated glomerular filtration rate showed up frequently; single metabolite SNPs were associated with more than one phenotype. Replications in independent samples were obtained for BMI and educational attainment. CONCLUSIONS Approximately 5-10% of the regions involved in the regulation of blood/urine metabolite levels seem to also play a role in BMI and mental traits/disorders and related phenotypes. If validated in metabolomic studies of the respective phenotypes, the associated blood/urine metabolites may enable novel preventive and therapeutic strategies.
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Affiliation(s)
- Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Triinu Peters
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dick Schijven
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Moritz Hebebrand
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Corinna Grasemann
- Pediatric Endocrinology and Diabetology, Klinik für Kinderheilkunde II, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas W Winkler
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Jochen Antel
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lisa Tegeler
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lena Brauner
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Roger A H Adan
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jurjen J Luykx
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Psychiatry, ZNA Hospitals, Antwerp, Belgium
| | - Christoph U Correll
- Division of Psychiatry Research, Northwell Health, The Zucker Hillside Hospital, Glen Oaks, NY, USA
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Luebeck, Luebeck, Schleswig-Holstein, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lars Libuda
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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31
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Abstract
Many potentially toxic electrophilic xenobiotics and some endogenous compounds are detoxified by conversion to the corresponding glutathione S-conjugate, which is metabolized to the N-acetylcysteine S-conjugate (mercapturate) and excreted. Some mercapturate pathway components, however, are toxic. Bioactivation (toxification) may occur when the glutathione S-conjugate (or mercapturate) is converted to a cysteine S-conjugate that undergoes a β-lyase reaction. If the sulfhydryl-containing fragment produced in this reaction is reactive, toxicity may ensue. Some drugs and halogenated workplace/environmental contaminants are bioactivated by this mechanism. On the other hand, cysteine S-conjugate β-lyases occur in nature as a means of generating some biologically useful sulfhydryl-containing compounds.
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32
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Xie J, Dong W, Liu R, Wang Y, Li Y. Research on the hepatotoxicity mechanism of citrate-modified silver nanoparticles based on metabolomics and proteomics. Nanotoxicology 2017; 12:18-31. [DOI: 10.1080/17435390.2017.1415389] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jiabin Xie
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Wenying Dong
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Rui Liu
- School of Chinese Materia Medica, Shanxi University of Traditional Chinese Medicine, Shanxi, PR China
| | - Yuming Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
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33
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Mol M, Regazzoni L, Altomare A, Degani G, Carini M, Vistoli G, Aldini G. Enzymatic and non-enzymatic detoxification of 4-hydroxynonenal: Methodological aspects and biological consequences. Free Radic Biol Med 2017; 111:328-344. [PMID: 28161307 DOI: 10.1016/j.freeradbiomed.2017.01.036] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
4-Hydroxynonenal (HNE), an electrophilic end-product deriving from lipid peroxidation, undergoes a heterogeneous set of biotransformations including enzymatic and non-enzymatic reactions. The former mostly involve red-ox reactions on the HNE oxygenated functions (phase I metabolism) and GSH conjugations (phase II) while the latter are due to the HNE capacity to spontaneously condense with nucleophilic sites within endogenous molecules such as proteins, nucleic acids and phospholipids. The overall metabolic fate of HNE has recently attracted great interest not only because it clearly determines the HNE disposal, but especially because the generated metabolites and adducts are not inactive molecules (as initially believed) but show biological activities even more pronounced than those of the parent compound as exemplified by potent pro-inflammatory stimulus induced by GSH conjugates. Similarly, several studies revealed that the non-enzymatic reactions, initially considered as damaging processes randomly involving all endogenous nucleophilic reactants, are in fact quite selective in terms of both reactivity of the nucleophilic sites and stability of the generated adducts. Even though many formed adducts retain the expected toxic consequences, some adducts exhibit well-defined beneficial roles as documented by the protective effects of sublethal concentrations of HNE against toxic concentrations of HNE. Clearly, future investigations are required to gain a more detailed understanding of the metabolic fate of HNE as well as to identify novel targets involved in the biological activity of the HNE metabolites. These studies are and will be permitted by the continuous progress in the analytical methods for the identification and quantitation of novel HNE metabolites as well as for proteomic analyses able to offer a comprehensive picture of the HNE-induced adducted targets. On these grounds, the present review will focus on the major enzymatic and non-enzymatic HNE biotransformations discussing both the molecular mechanisms involved and the biological effects elicited. The review will also describe the most important analytical enhancements that have permitted the here discussed advancements in our understanding of the HNE metabolic fate and which will permit in a near future an even better knowledge of this enigmatic molecule.
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Affiliation(s)
- Marco Mol
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Luca Regazzoni
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Alessandra Altomare
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Genny Degani
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Marina Carini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
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34
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Sakai C, Iwano S, Shimizu M, Onodera J, Uchida M, Sakurada E, Yamazaki Y, Asaoka Y, Imura N, Uno Y, Murayama N, Hayashi R, Yamazaki H, Miyamoto Y. Analysis of gene expression for microminipig liver transcriptomes using parallel long-read technology and short-read sequencing. Biopharm Drug Dispos 2017; 37:220-32. [PMID: 27214158 DOI: 10.1002/bdd.2007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/22/2016] [Accepted: 02/22/2016] [Indexed: 11/10/2022]
Abstract
The microminipig is one of the smallest minipigs that has emerged as a possible experimental animal model, because it shares many anatomical and/or physiological similarities with humans, including the coronary artery distribution in the heart, the digestive physiology, the kidney size and its structure, and so on. However, information on gene expression profiles, including those on drug-metabolizing phase I and II enzymes, in the microminipig is limited. Therefore, the aim of the present study was to identify transcripts in microminipig livers and to determine gene expression profiles. De novo assembly and expression analyses of microminipig transcripts were conducted with liver samples from three male and three female microminipigs using parallel long-read and short-read sequencing technologies. After unique sequences had been automatically aligned by assembling software, the mean contig length of 50843 transcripts was 707 bp. The expression profiles of cytochrome P450 (P450) 1A2, 2C, 2E1 and 3A genes in livers in microminipigs were similar to those in humans. Liver carboxylesterase (CES) precursor, liver CES-like, UDP-glucuronosyltransferase (UGT) 2C1-like, amine sulfotransferase (SULT)-like, N-acetyltransferases (NAT8) and glutathione S-transferase (GST) A2 genes, which are relatively unknown genes in pigs and/or humans, were expressed strongly. Furthermore, no significant gender differences were observed in the gene expression profiles of phase I enzymes, whereas UGT2B17, SULT1E1, SULT2A1, amine SULT-like, NAT8 and GSTT4 genes were different between males and females among phase II enzyme genes under the present sample conditions. These results provide a foundation for mechanistic studies and the use of microminipigs as model animals for drug development in the future. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Chizuka Sakai
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Shunsuke Iwano
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan.,Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan
| | - Makiko Shimizu
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan
| | - Jun Onodera
- Eurofins Genomics K.K., Ohta-ku, Tokyo, 143-0003, Japan
| | - Masashi Uchida
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Eri Sakurada
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Yuri Yamazaki
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Yoshiji Asaoka
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Naoko Imura
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories, Ltd, Kainan, Wakayama, Japan
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan
| | - Ryoji Hayashi
- Toxicology and Pharmacokinetics Laboratories, Pharmaceutical Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, 248-8555, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan
| | - Yohei Miyamoto
- Pharmaceutical Clinical Research Department, Toray Industries, Inc., 1-1, Nihonbashi-muromachi 2-chome, Chuo-ku, Tokyo, 103-8666, Japan
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Guo Y, Cui JY, Lu H, Klaassen CD. Effect of nine diets on mRNAs of phase-II conjugation enzymes in livers of mice. Xenobiotica 2016; 47:645-654. [PMID: 27686132 DOI: 10.1080/00498254.2016.1213926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
1. Phase-II enzymes are important in metabolizing many xenobiotics including prescription drugs and chemical carcinogens. Whereas it is known that diet can alter the expression of phase-II conjugation enzymes, the previous studies are limited in using only two or three diets and examining only a few enzymes. 2. Adult male C57BL6 mice were fed one of nine diets for 3 weeks. Of the 87 genes encoding major hepatic phase-II enzymes, approximately one-half (43) were altered by at least one diet. Diet restriction altered the hepatic expression of the most genes encoding phase-II enzymes (27), followed by lab chow (15), atherogenic diet (13), high-fat diet (10), western diet (7), high-fructose diet (5), and essential fatty acid-deficient diet (3), whereas the low n-3 fatty acid diet had no effect on the hepatic expression of these phase-II enzymes. 3. This comprehensive study provides detailed information on which conjugation enzymes are changed by these diets, and these data can be used to further investigate the mechanism for these changes in messenger RNAs, and whether these changes result in alterations in enzyme activity and drug action.
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Affiliation(s)
- Ying Guo
- a Department of Internal Medicine , University of Kansas Medical Center , Kansas City, KS , USA.,b Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , P.R. China , and
| | - Julia Yue Cui
- a Department of Internal Medicine , University of Kansas Medical Center , Kansas City, KS , USA
| | - Hong Lu
- a Department of Internal Medicine , University of Kansas Medical Center , Kansas City, KS , USA.,c Department of Pharmacology , SUNY Upstate Medical University , Syracuse, NY , USA
| | - Curtis D Klaassen
- a Department of Internal Medicine , University of Kansas Medical Center , Kansas City, KS , USA
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Deol R, Josephy PD. Acetylation of aromatic cysteine conjugates by recombinant human N-acetyltransferase 8. Xenobiotica 2016; 47:202-207. [DOI: 10.1080/00498254.2016.1178410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Reema Deol
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - P. David Josephy
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Groten CJ, Rebane JT, Hodgson HM, Chauhan AK, Blohm G, Magoski NS. Ca2+ removal by the plasma membrane Ca2+-ATPase influences the contribution of mitochondria to activity-dependent Ca2+ dynamics in Aplysia neuroendocrine cells. J Neurophysiol 2016; 115:2615-34. [PMID: 26864756 DOI: 10.1152/jn.00494.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 02/04/2016] [Indexed: 01/05/2023] Open
Abstract
After Ca(2+) influx, mitochondria can sequester Ca(2+) and subsequently release it back into the cytosol. This form of Ca(2+)-induced Ca(2+) release (CICR) prolongs Ca(2+) signaling and can potentially mediate activity-dependent plasticity. As Ca(2+) is required for its subsequent release, Ca(2+) removal systems, like the plasma membrane Ca(2+)-ATPase (PMCA), could impact CICR. Here we examine such a role for the PMCA in the bag cell neurons of Aplysia californica CICR is triggered in these neurons during an afterdischarge and is implicated in sustaining membrane excitability and peptide secretion. Somatic Ca(2+) was measured from fura-PE3-loaded cultured bag cell neurons recorded under whole cell voltage clamp. Voltage-gated Ca(2+) influx was elicited with a 5-Hz, 1-min train, which mimics the fast phase of the afterdischarge. PMCA inhibition with carboxyeosin or extracellular alkalization augmented the effectiveness of Ca(2+) influx in eliciting mitochondrial CICR. A Ca(2+) compartment model recapitulated these findings and indicated that disrupting PMCA-dependent Ca(2+) removal increases CICR by enhancing mitochondrial Ca(2+) loading. Indeed, carboxyeosin augmented train-evoked mitochondrial Ca(2+) uptake. Consistent with their role on Ca(2+) dynamics, cell labeling revealed that the PMCA and mitochondria overlap with Ca(2+) entry sites. Finally, PMCA-dependent Ca(2+) extrusion did not impact endoplasmic reticulum-dependent Ca(2+) removal or release, despite the organelle residing near Ca(2+) entry sites. Our results demonstrate that Ca(2+) removal by the PMCA influences the propensity for stimulus-evoked CICR by adjusting the amount of Ca(2+) available for mitochondrial Ca(2+) uptake. This study highlights a mechanism by which the PMCA could impact activity-dependent plasticity in the bag cell neurons.
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Affiliation(s)
- Christopher J Groten
- Department of Biomedical and Molecular Sciences, Physiology Graduate Program, Queen's University, Kingston, Ontario, Canada
| | - Jonathan T Rebane
- Department of Biomedical and Molecular Sciences, Physiology Graduate Program, Queen's University, Kingston, Ontario, Canada
| | - Heather M Hodgson
- Department of Biomedical and Molecular Sciences, Physiology Graduate Program, Queen's University, Kingston, Ontario, Canada
| | - Alamjeet K Chauhan
- Department of Biomedical and Molecular Sciences, Physiology Graduate Program, Queen's University, Kingston, Ontario, Canada
| | - Gunnar Blohm
- Department of Biomedical and Molecular Sciences, Physiology Graduate Program, Queen's University, Kingston, Ontario, Canada
| | - Neil S Magoski
- Department of Biomedical and Molecular Sciences, Physiology Graduate Program, Queen's University, Kingston, Ontario, Canada
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Karmodiya K, Anamika K, Muley V, Pradhan SJ, Bhide Y, Galande S. Camello, a novel family of Histone Acetyltransferases that acetylate histone H4 and is essential for zebrafish development. Sci Rep 2014; 4:6076. [PMID: 25123547 PMCID: PMC4133703 DOI: 10.1038/srep06076] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/07/2014] [Indexed: 12/04/2022] Open
Abstract
In this study, we have investigated genome-wide occurrence of Histone Acetyltransferases (HATs) in genomes of Mus musculus and Danio rerio on the basis of presence of HAT domain. Our study identified a group of proteins that lacks characteristic features of known HAT families, relatively smaller in size and has no other associated domains. Most of the proteins in this unclassified group are Camello proteins, which are not yet known and classified as functional HATs. Our in vitro and in vivo analysis revealed that Camello family proteins are active HATs and exhibit specificity towards histone H4. Interestingly, Camello proteins are among the first identified HATs showing perinuclear localization. Moreover, Camello proteins are evolutionarily conserved in all chordates and are observed for the first time in cnidarians in phylogeny. Furthermore, knockdown of Camello protein (CMLO3) in zebrafish embryos exhibited defects in axis elongation and head formation. Thus, our study identified a novel family of active HATs that is specific for histone H4 acetylation, exhibits perinuclear localization and is essential for zebrafish development.
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Affiliation(s)
- Krishanpal Karmodiya
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 021, India
| | - Krishanpal Anamika
- 1] Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 021, India [2]
| | - Vijaykumar Muley
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 021, India
| | - Saurabh J Pradhan
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 021, India
| | - Yoshita Bhide
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 021, India
| | - Sanjeev Galande
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 021, India
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Fu J, Zhang H, Zhuang Y, Liu H, Shi Q, Li D, Ju X. The role of N-acetyltransferase 8 in mesenchymal stem cell-based therapy for liver ischemia/reperfusion injury in rats. PLoS One 2014; 9:e103355. [PMID: 25057902 PMCID: PMC4109999 DOI: 10.1371/journal.pone.0103355] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/29/2014] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To evaluate the impact of mesenchymal stem cells (MSCs) against hepatic I/R injury and explore the role of N-acetyltransferase 8 (NAT8) in the process. METHODS We investigated the potential of injected MSCs systemically via the tail vein in healing injuried liver of the SD rat model of 70% hepatic I/R injury by measuring the biochemical and pathologic alterations. Subsequently, we evaluated the expression levels of NAT8 by western blotting in vivo. Concurrently, hydrogen peroxide (H2O2)-induced apoptosis in the human normal liver cell line L02 was performed in vitro to evaluate the protective effects of MSC conditioned medium (MSC-CM) on L02 cells. In addition, we downregulated and upregulated NAT8 expression in L02 cells and induced apoptosis by using H2O2 to study the protective role of NAT8. RESULTS MSCs implantation led to a significant reduced liver enzyme levels, an advanced protection in the histopathological findings of the acutely injured liver and a significantly lower percentage of TUNEL-positive cells, which were increased after I/R injury. In vitro assays, MSC-CM inhibited hepatocyte apoptosis induced by H2O2. Moreover, overexpression or downregulation of NAT8 prevented or aggravated hepatocyte apoptosis induced by H2O2, respectively. CONCLUSIONS MSC transplantation provides support to the I/R-injured liver by inhibiting hepatocellular apoptosis and stimulating NAT8 regeneration.
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Affiliation(s)
- Jinqiu Fu
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
| | - Haiyan Zhang
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
| | - Yong Zhuang
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
| | - Huan Liu
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
| | - Qing Shi
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
| | - Dong Li
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
- * E-mail: (XJ); (DL)
| | - Xiuli Ju
- Department of Pediatrics, Qilu Hospital, Shandong University, Jinan, P.R. China
- * E-mail: (XJ); (DL)
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Veiga-da-Cunha M, Chevalier N, Stroobant V, Vertommen D, Van Schaftingen E. Metabolite proofreading in carnosine and homocarnosine synthesis: molecular identification of PM20D2 as β-alanyl-lysine dipeptidase. J Biol Chem 2014; 289:19726-36. [PMID: 24891507 DOI: 10.1074/jbc.m114.576579] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carnosine synthase is the ATP-dependent ligase responsible for carnosine (β-alanyl-histidine) and homocarnosine (γ-aminobutyryl-histidine) synthesis in skeletal muscle and brain, respectively. This enzyme uses, also at substantial rates, lysine, ornithine, and arginine instead of histidine, yet the resulting dipeptides are virtually absent from muscle or brain, suggesting that they are removed by a "metabolite repair" enzyme. Using a radiolabeled substrate, we found that rat skeletal muscle, heart, and brain contained a cytosolic β-alanyl-lysine dipeptidase activity. This enzyme, which has the characteristics of a metalloenzyme, was purified ≈ 200-fold from rat skeletal muscle. Mass spectrometry analysis of the fractions obtained at different purification stages indicated parallel enrichment of PM20D2, a peptidase of unknown function belonging to the metallopeptidase 20 family. Western blotting showed coelution of PM20D2 with β-alanyl-lysine dipeptidase activity. Recombinant mouse PM20D2 hydrolyzed β-alanyl-lysine, β-alanyl-ornithine, γ-aminobutyryl-lysine, and γ-aminobutyryl-ornithine as its best substrates. It also acted at lower rates on β-alanyl-arginine and γ-aminobutyryl-arginine but virtually not on carnosine or homocarnosine. Although acting preferentially on basic dipeptides derived from β-alanine or γ-aminobutyrate, PM20D2 also acted at lower rates on some "classic dipeptides" like α-alanyl-lysine and α-lysyl-lysine. The same activity profile was observed with human PM20D2, yet this enzyme was ∼ 100-200-fold less active on all substrates tested than the mouse enzyme. Cotransfection in HEK293T cells of mouse or human PM20D2 together with carnosine synthase prevented the accumulation of abnormal dipeptides (β-alanyl-lysine, β-alanyl-ornithine, γ-aminobutyryl-lysine), thus favoring the synthesis of carnosine and homocarnosine and confirming the metabolite repair role of PM20D2.
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Affiliation(s)
| | | | | | - Didier Vertommen
- the Protein Phosphorylation Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
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Yu B, Zheng Y, Alexander D, Morrison AC, Coresh J, Boerwinkle E. Genetic determinants influencing human serum metabolome among African Americans. PLoS Genet 2014; 10:e1004212. [PMID: 24625756 PMCID: PMC3952826 DOI: 10.1371/journal.pgen.1004212] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 01/13/2014] [Indexed: 11/18/2022] Open
Abstract
Phenotypes proximal to gene action generally reflect larger genetic effect sizes than those that are distant. The human metabolome, a result of multiple cellular and biological processes, are functional intermediate phenotypes proximal to gene action. Here, we present a genome-wide association study of 308 untargeted metabolite levels among African Americans from the Atherosclerosis Risk in Communities (ARIC) Study. Nineteen significant common variant-metabolite associations were identified, including 13 novel loci (p<1.6×10−10). These loci were associated with 7–50% of the difference in metabolite levels per allele, and the variance explained ranged from 4% to 20%. Fourteen genes were identified within the nineteen loci, and four of them contained non-synonymous substitutions in four enzyme-encoding genes (KLKB1, SIAE, CPS1, and NAT8); the other significant loci consist of eight other enzyme-encoding genes (ACE, GATM, ACY3, ACSM2B, THEM4, ADH4, UGT1A, TREH), a transporter gene (SLC6A13) and a polycystin protein gene (PKD2L1). In addition, four potential disease-associated paths were identified, including two direct longitudinal predictive relationships: NAT8 with N-acetylornithine, N-acetyl-1-methylhistidine and incident chronic kidney disease, and TREH with trehalose and incident diabetes. These results highlight the value of using endophenotypes proximal to gene function to discover new insights into biology and disease pathology. Most contemporary GWAS studies have achieved increased power by increasing the size of the discovery sample to tens of thousands of individuals. An alternative approach for detecting the effects of novel loci is to measure phenotypes that more immediately reflect the effects of gene function. The metabolome consists of a collection of small molecules resulting from a variety of cellular and biologic processes, which can be considered intermediate phenotypes proximal to gene function. Here, we report a genome-wide association study identifying nineteen genetic loci influencing untargeted metabolomes traits among African Americans in the Atherosclerosis Risk in Communities (ARIC) Study. Fourteen genes mapped within nineteen loci, including twelve enzyme-encoding genes (KLKB1, SIAE, CPS1, NAT8, ACE, GATM, ACY3, ACSM2B, THEM4, ADH4, UGT1A and TREH), a transporter gene (SLC6A13) and a polycystin protein gene (PKD2L1). In addition, four potential disease-associated paths were identified, including two direct longitudinal predictive relationships: NAT8 with N-acetylornithine, N-acetyl-1-methylhistidine and incident chronic kidney disease, and TREH with trehalose and incident diabetes. These results highlight the value of using phenotypes proximal to gene function to promote novel gene discovery.
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Affiliation(s)
- Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yan Zheng
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Danny Alexander
- Metabolon, Inc., Durham, North Carolina, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Marlaire S, Van Schaftingen E, Veiga-da-Cunha M. C7orf10 encodes succinate-hydroxymethylglutarate CoA-transferase, the enzyme that converts glutarate to glutaryl-CoA. J Inherit Metab Dis 2014; 37:13-9. [PMID: 23893049 DOI: 10.1007/s10545-013-9632-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/14/2013] [Accepted: 06/21/2013] [Indexed: 10/26/2022]
Abstract
Glutarate, a side-product in the metabolism of tryptophan and lysine, is metabolized by conversion to glutaryl-CoA by a transferase using succinyl-CoA as a coenzyme donor. The enzyme catalyzing this conversion has not been formally identified. However, a benign form of glutaric aciduria (glutaric aciduria type III) is due to mutations in C7orf10, a putative member of the coenzyme A transferase class III family. In the present work, we show that recombinant human C7orf10 catalyzes the succinyl-CoA-dependent conversion of glutarate to glutaryl-CoA. C7orf10 could use many dicarboxylic acids as CoA acceptors, the best ones being glutarate, succinate, adipate, and 3-hydroxymethylglutarate. Confocal microscopy analysis of CHO cells transfected with a C7orf10-GFP fusion protein indicated that C7orf10 is a mitochondrial protein, in agreement with the presence of a predicted mitochondrial propeptide at its N-terminus. The effect of a missense mutation (p.Arg336Trp) found in the homozygous state in several patients with glutaric aciduria type III and present in the general population at a low frequency was also investigated. The p.Arg336Trp mutation led to the production of insoluble and inactive C7orf10 both in Escherichia coli and in HEK293T cells. These findings indicate that C7orf10 is implicated in the metabolism of glutarate, but possibly also of longer dicarboxylic acids. Homologues of this enzyme are found in numerous bacterial operons comprising also a putative glutaryl-CoA dehydrogenase, indicating that an enzyme with similar specificity exists in prokaryotes.
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Affiliation(s)
- Simon Marlaire
- de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium,
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Veiga-da-Cunha M, Verhoeven-Duif NM, de Koning TJ, Duran M, Dorland B, Van Schaftingen E. Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria. J Inherit Metab Dis 2013; 36:961-6. [PMID: 23242558 DOI: 10.1007/s10545-012-9568-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Phosphohydroxylysinuria has been described in two patients with neurological symptoms, but the deficient enzyme or mutated gene has never been identified. In the present work, we tested the hypothesis that this condition is due to mutations in the AGXT2L2 gene, recently shown to encode phosphohydroxylysine phospholyase. DNA analysis from a third patient, without neurological symptoms, but with an extreme hyperlaxicity of the joints, shows the existence of two mutations, p. Gly240Arg and p.Glu437Val, both in the heterozygous state. Sequencing of cDNA clones derived from fibroblasts mRNA indicated that the two mutations were allelic. Both mutations replace conserved residues. The mutated proteins were produced as recombinant proteins in Escherichia coli and HEK293T cells and shown to be very largely insoluble, whereas the wild-type one was produced as a soluble and active protein. We conclude that phosphohydroxylysinuria is due to mutations in the AGXT2L2 gene and the resulting lack of activity of phosphohydroxylysine phospholyase in vivo. The finding that the nul alleles of p.Gly240Arg and p.Glu437Val are present at low frequencies in the European and/or North American population suggests that this condition is more common than previously thought. The diversity of the clinical symptoms described in three patients with phosphohydroxylysinuria indicates that this is most likely not a neurometabolic disease.
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Affiliation(s)
- Maria Veiga-da-Cunha
- Laboratory of Physiological Chemistry, de Duve Institute and Université Catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium,
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Rychtrmoc D, Hubálková L, Víšková A, Libra A, Bunček M, Červinková Z. Transcriptome temporal and functional analysis of liver regeneration termination. Physiol Res 2013; 61:S77-92. [PMID: 23130906 DOI: 10.33549/physiolres.932393] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Decades of liver regeneration studies still left the termination phase least elucidated. However regeneration ending mechanisms are clinicaly relevant. We aimed to analyse the timing and transcriptional control of the latest phase of liver regeneration, both controversial. Male Wistar rats were subjected to 2/3 partial hepatectomy with recovery lasting from 1 to 14 days. Time-series microarray data were assessed by innovative combination of hierarchical clustering and principal component analysis and validated by real-time RT-PCR. Hierarchical clustering and principal component analysis in agreement distinguished three temporal phases of liver regeneration. We found 359 genes specifically altered during late phase regeneration. Gene enrichment analysis and manual review of microarray data suggested five pathways worth further study: PPAR signalling pathway; lipid metabolism; complement, coagulation and fibrinolytic cascades; ECM remodelling and xenobiotic biotransformation. Microarray findings pertinent for termination phase were substantiated by real-time RT-PCR. In conclusion, transcriptional profiling mapped late phase of liver regeneration beyond 5(th) day of recovery and revealed 5 pathways specifically acting at this time. Inclusion of longer post-surgery intervals brought improved coverage of regeneration time dynamics and is advisable for further works. Investigation into the workings of suggested pathways might prove helpful in preventing and managing liver tumours.
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Affiliation(s)
- D Rychtrmoc
- Department of Physiology, Faculty of Medicine in Hradec Králové, Charles University in Prague, Hradec Králové, Czech Republic.
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46
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Donor substrate specificity of bovine kidney gamma-glutamyltransferase. Chem Biol Interact 2013; 203:480-5. [DOI: 10.1016/j.cbi.2013.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/18/2013] [Accepted: 02/26/2013] [Indexed: 11/20/2022]
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47
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Lu H, Gunewardena S, Cui JY, Yoo B, Zhong XB, Klaassen CD. RNA-sequencing quantification of hepatic ontogeny and tissue distribution of mRNAs of phase II enzymes in mice. Drug Metab Dispos 2013; 41:844-57. [PMID: 23382457 DOI: 10.1124/dmd.112.050211] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Phase II conjugating enzymes play key roles in the metabolism of xenobiotics. In the present study, RNA sequencing was used to elucidate hepatic ontogeny and tissue distribution of mRNA expression of all major known Phase II enzymes, including enzymes involved in glucuronidation, sulfation, glutathione conjugation, acetylation, methylation, and amino acid conjugation, as well as enzymes for the synthesis of Phase II cosubstrates, in male C57BL/6J mice. Livers from male C57BL/6J mice were collected at 12 ages from prenatal to adulthood. Many of these Phase II enzymes were expressed at much higher levels in adult livers than in perinatal livers, such as Ugt1a6b, -2a3, -2b1, -2b5, -2b36, -3a1, and -3a2; Gsta1, -m1, -p1, -p2, and -z1; mGst1; Nat8; Comt; Nnmt; Baat; Ugdh; and Gclc. In contrast, hepatic mRNA expression of a few Phase II enzymes decreased during postnatal liver development, such as mGst2, mGst3, Gclm, and Mat2a. Hepatic expression of certain Phase II enzymes peaked during the adolescent stage, such as Ugt1a1, Sult1a1, Sult1c2, Sult1d1, Sult2as, Sult5a1, Tpmt, Glyat, Ugp2, and Mat1a. In adult mice, the total transcripts for Phase II enzymes were comparable in liver, kidney, and small intestine; however, individual Phase II enzymes displayed marked tissue specificity among the three organs. In conclusion, this study unveils for the first time developmental changes in mRNA abundance of all major known Phase II enzymes in mouse liver, as well as their tissue-specific expression in key drug-metabolizing organs. The age- and tissue-specific expression of Phase II enzymes indicate that the detoxification of xenobiotics is highly regulated by age and cell type.
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Affiliation(s)
- Hong Lu
- Department of Pharmacology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA.
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Sterz K, Scherer G, Krumsiek J, Theis FJ, Ecker J. Identification and Quantification of 1-Hydroxybutene-2-yl Mercapturic Acid in Human Urine by UPLC- HILIC-MS/MS as a Novel Biomarker for 1,3-Butadiene Exposure. Chem Res Toxicol 2012; 25:1565-7. [DOI: 10.1021/tx3002862] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Katharina Sterz
- ABF Analytisch-Biologisches Forschungslabor GmbH, 80336 Munich, Germany
| | - Gerhard Scherer
- ABF Analytisch-Biologisches Forschungslabor GmbH, 80336 Munich, Germany
| | - Jan Krumsiek
- Institute of Bioinformatics
and Systems Biology, Helmholtz Zentrum Munich, 85764 Neuherberg, Germany
| | - Fabian J. Theis
- Institute of Bioinformatics
and Systems Biology, Helmholtz Zentrum Munich, 85764 Neuherberg, Germany
| | - Josef Ecker
- ABF Analytisch-Biologisches Forschungslabor GmbH, 80336 Munich, Germany
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Poon JCH, Josephy PD. Hydrolysis of S-aryl-cysteinylglycine conjugates catalyzed by porcine kidney cortex membrane dipeptidase. Xenobiotica 2012; 42:1178-86. [DOI: 10.3109/00498254.2012.700427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Determinants of the enzymatic activity and the subcellular localization of aspartate N-acetyltransferase. Biochem J 2011; 441:105-12. [DOI: 10.1042/bj20111179] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aspartate N-acetyltransferase (NAT8L, N-acetyltransferase 8-like), the enzyme that synthesizes N-acetylaspartate, is membrane-bound and is at least partially associated with the ER (endoplasmic reticulum). The aim of the present study was to determine which regions of the protein are important for its catalytic activity and its subcellular localization. Transfection of truncated forms of NAT8L into HEK (human embryonic kidney)-293T cells indicated that the 68 N-terminal residues (regions 1 and 2) have no importance for the catalytic activity and the subcellular localization of this enzyme, which was exclusively associated with the ER. Mutation of conserved residues that precede (Arg81 and Glu101, in region 3) or follow (Asp168 and Arg220, in region 5) the putative membrane region (region 4) markedly affected the kinetic properties, suggesting that regions 3 and 5 form the catalytic domain and that the membrane region has a loop structure. Evidence is provided for the membrane region comprising α-helices and the catalytic site being cytosolic. Transfection of chimaeric proteins in which GFP (green fluorescent protein) was fused to different regions of NAT8L indicated that the membrane region (region 4) is necessary and sufficient to target NAT8L to the ER. Thus NAT8L is targeted to the ER membrane by a hydrophobic loop that connects two regions of the catalytic domain.
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