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Thomas TA, Francis RO, Zimring JC, Kao JP, Nemkov T, Spitalnik SL. The Role of Ergothioneine in Red Blood Cell Biology: A Review and Perspective. Antioxidants (Basel) 2024; 13:717. [PMID: 38929156 PMCID: PMC11200860 DOI: 10.3390/antiox13060717] [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: 05/16/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Oxidative stress can damage tissues and cells, and their resilience or susceptibility depends on the robustness of their antioxidant mechanisms. The latter include small molecules, proteins, and enzymes, which are linked together in metabolic pathways. Red blood cells are particularly susceptible to oxidative stress due to their large number of hemoglobin molecules, which can undergo auto-oxidation. This yields reactive oxygen species that participate in Fenton chemistry, ultimately damaging their membranes and cytosolic constituents. Fortunately, red blood cells contain robust antioxidant systems to enable them to circulate and perform their physiological functions, particularly delivering oxygen and removing carbon dioxide. Nonetheless, if red blood cells have insufficient antioxidant reserves (e.g., due to genetics, diet, disease, or toxin exposure), this can induce hemolysis in vivo or enhance susceptibility to a "storage lesion" in vitro, when blood donations are refrigerator-stored for transfusion purposes. Ergothioneine, a small molecule not synthesized by mammals, is obtained only through the diet. It is absorbed from the gut and enters cells using a highly specific transporter (i.e., SLC22A4). Certain cells and tissues, particularly red blood cells, contain high ergothioneine levels. Although no deficiency-related disease has been identified, evidence suggests ergothioneine may be a beneficial "nutraceutical." Given the requirements of red blood cells to resist oxidative stress and their high ergothioneine content, this review discusses ergothioneine's potential importance in protecting these cells and identifies knowledge gaps regarding its relevance in enhancing red blood cell circulatory, storage, and transfusion quality.
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Affiliation(s)
- Tiffany A. Thomas
- Laboratory of Transfusion Biology, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; (T.A.T.)
| | - Richard O. Francis
- Laboratory of Transfusion Biology, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; (T.A.T.)
| | - James C. Zimring
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Joseph P. Kao
- Center for Biomedical Engineering, Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Denver, CO 80203, USA
| | - Steven L. Spitalnik
- Laboratory of Transfusion Biology, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; (T.A.T.)
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Membrez M, Migliavacca E, Christen S, Yaku K, Trieu J, Lee AK, Morandini F, Giner MP, Stiner J, Makarov MV, Garratt ES, Vasiloglou MF, Chanvillard L, Dalbram E, Ehrlich AM, Sanchez-Garcia JL, Canto C, Karagounis LG, Treebak JT, Migaud ME, Heshmat R, Razi F, Karnani N, Ostovar A, Farzadfar F, Tay SKH, Sanders MJ, Lillycrop KA, Godfrey KM, Nakagawa T, Moco S, Koopman R, Lynch GS, Sorrentino V, Feige JN. Trigonelline is an NAD + precursor that improves muscle function during ageing and is reduced in human sarcopenia. Nat Metab 2024; 6:433-447. [PMID: 38504132 DOI: 10.1038/s42255-024-00997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/26/2024] [Indexed: 03/21/2024]
Abstract
Mitochondrial dysfunction and low nicotinamide adenine dinucleotide (NAD+) levels are hallmarks of skeletal muscle ageing and sarcopenia1-3, but it is unclear whether these defects result from local changes or can be mediated by systemic or dietary cues. Here we report a functional link between circulating levels of the natural alkaloid trigonelline, which is structurally related to nicotinic acid4, NAD+ levels and muscle health in multiple species. In humans, serum trigonelline levels are reduced with sarcopenia and correlate positively with muscle strength and mitochondrial oxidative phosphorylation in skeletal muscle. Using naturally occurring and isotopically labelled trigonelline, we demonstrate that trigonelline incorporates into the NAD+ pool and increases NAD+ levels in Caenorhabditis elegans, mice and primary myotubes from healthy individuals and individuals with sarcopenia. Mechanistically, trigonelline does not activate GPR109A but is metabolized via the nicotinate phosphoribosyltransferase/Preiss-Handler pathway5,6 across models. In C. elegans, trigonelline improves mitochondrial respiration and biogenesis, reduces age-related muscle wasting and increases lifespan and mobility through an NAD+-dependent mechanism requiring sirtuin. Dietary trigonelline supplementation in male mice enhances muscle strength and prevents fatigue during ageing. Collectively, we identify nutritional supplementation of trigonelline as an NAD+-boosting strategy with therapeutic potential for age-associated muscle decline.
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Affiliation(s)
- Mathieu Membrez
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | | | - Stefan Christen
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Keisuke Yaku
- Department of Molecular and Medical Pharmacology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Jennifer Trieu
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Alaina K Lee
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Francesco Morandini
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maria Pilar Giner
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Jade Stiner
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mikhail V Makarov
- Mitchell Cancer Institute, Department of Pharmacology, F. P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Emma S Garratt
- Institute of Developmental Sciences, Human Developmental and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research, Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Maria F Vasiloglou
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Lucie Chanvillard
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Emilie Dalbram
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amy M Ehrlich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Carles Canto
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Leonidas G Karagounis
- Nestlé Health Science, Translation Research, Lausanne, Switzerland
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie E Migaud
- Mitchell Cancer Institute, Department of Pharmacology, F. P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Ramin Heshmat
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Farideh Razi
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Science Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Afshin Ostovar
- Osteoporosis Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Farshad Farzadfar
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Stacey K H Tay
- KTP-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Matthew J Sanders
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Karen A Lillycrop
- Institute of Developmental Sciences, Human Developmental and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research, Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Keith M Godfrey
- Institute of Developmental Sciences, Human Developmental and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research, Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Takashi Nakagawa
- Department of Molecular and Medical Pharmacology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Sofia Moco
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - René Koopman
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Vincenzo Sorrentino
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Jerome N Feige
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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Kondoh H, Kameda M. Metabolites in aging and aging-relevant diseases: Frailty, sarcopenia and cognitive decline. Geriatr Gerontol Int 2024; 24 Suppl 1:44-48. [PMID: 37837183 DOI: 10.1111/ggi.14684] [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: 08/11/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
Aging shows biologically complex features with high individual variability, which reflects the exposure to several stimuli and the adaptation to them. Among them, metabolic changes are well observed as consequences or possible causes of aging. Calorie restriction extends organismal life span in experimental models. Several metabolites; for example, resveratrol or nicotinamide mononucleotide, are reported to mimic calorie restriction effects in vivo. Metabolomic research would be useful to evaluate metabolites as biomarkers in aging-relevant events and to identify metabolic regulation of aging. We recently developed the metabolomic approach for whole blood analysis, which functions as strong tool for this purpose. We review the update findings in aging-relevant metabolites detected by this method. Geriatr Gerontol Int 2024; 24: 44-48.
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Affiliation(s)
- Hiroshi Kondoh
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Kameda
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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4
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Zhan H, Wan Y, Sun Y, Xu Z, Zhang F, Yang K, Zhu W, Cheung CP, Tang W, Ng EK, Wong SK, Yeoh YK, Kl Chan F, Miao Y, Zuo T, Zeng Z, Ng SC. Gut mycobiome alterations in obesity in geographically different regions. Gut Microbes 2024; 16:2367297. [PMID: 38899956 PMCID: PMC11195487 DOI: 10.1080/19490976.2024.2367297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
The gut fungi play important roles in human health and are involved in energy metabolism. This study aimed to examine gut mycobiome composition in obese subjects in two geographically different regions in China and to identify specific gut fungi associated with obesity. A total of 217 subjects from two regions with different urbanization levels [Hong Kong (HK): obese, n = 59; lean, n = 59; Kunming (KM): obese, n = 50; lean, n = 49. Mean body mass index (BMI) for obesity = 33.7] were recruited. We performed deep shotgun metagenomic sequencing on fecal samples to compare gut mycobiome composition and trophic functions in lean and obese subjects across these two regions. The gut mycobiome of obese subjects in both HK and KM were altered compared to those of lean subjects, characterized by a decrease in the relative abundance of Nakaseomyces, Schizosaccharomyces pombe, Candida dubliniensis and an increase in the abundance of Lanchanceathermotolerans, Saccharomyces paradox, Parastagonospora nodorum and Myceliophthorathermophila. Reduced fungal - bacterial and fungal - fungal correlations as well as increased negative fungal-bacterial correlations were observed in the gut of obese subjects. Furthermore, the anti-obesity effect of fungus S. pombe was further validated using a mouse model. Supplementing high-fat diet-induced obese mice with the fungus for 12 weeks led to a significant reduction in body weight gain (p < 0.001), and an improvement in lipid and glucose metabolism compared to mice without intervention. In conclusion, the gut mycobiome composition and functionalities of obese subjects were altered. These data shed light on the potential of utilizing fungus-based therapeutics for the treatment of obesity. S. pombe may serve as a potential fungal probiotic in the prevention of diet-induced obesity and future human trials are needed.
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Affiliation(s)
- Hui Zhan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yating Wan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Yunnan, China
- Yunnan Geriatric Medical Center, Kunming, Yunnan, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fen Zhang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Keli Yang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenyi Zhu
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
| | - Enders Kw Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Simon Kh Wong
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
| | - Francis Kl Chan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Yunnan, China
| | - Tao Zuo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhong Zeng
- Department of Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Siew C Ng
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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5
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Wang P, Chen M, Hou Y, Luan J, Liu R, Chen L, Hu M, Yu Q. Fingerstick blood assay maps real-world NAD + disparity across gender and age. Aging Cell 2023; 22:e13965. [PMID: 37641521 PMCID: PMC10577551 DOI: 10.1111/acel.13965] [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: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+ ) level has been associated with various age-related diseases and its pharmacological modulation emerges as a potential approach for aging intervention. But human NAD+ landscape exhibits large heterogeneity. The lack of rapid, low-cost assays limits the establishment of whole-blood NAD+ baseline and the development of personalized therapies, especially for those with poor responses towards conventional NAD+ supplementations. Here, we developed an automated NAD+ analyzer for the rapid measurement of NAD+ with 5 μL of capillary blood using recombinant bioluminescent sensor protein and automated optical reader. The minimal invasiveness of the assay allowed a frequent and decentralized mapping of real-world NAD+ dynamics. We showed that aerobic sport and NMN supplementation increased whole-blood NAD+ and that male on average has higher NAD+ than female before the age of 50. We further revealed the long-term stability of human NAD+ baseline over 100 days and identified major real-world NAD+ -modulating behaviors.
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Affiliation(s)
- Pei Wang
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
| | - Meiting Chen
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
| | - Yaying Hou
- Celfull (China) Operation and Research CenterShenzhenChina
| | - Jun Luan
- Department of Sports MedicineGuangzhou Sport UniversityGuangzhouChina
| | - Ruili Liu
- Celfull (China) Operation and Research CenterShenzhenChina
| | - Liuqing Chen
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
| | - Min Hu
- Department of Sports MedicineGuangzhou Sport UniversityGuangzhouChina
| | - Qiuliyang Yu
- Sino‐European Center of Biomedicine and Health, Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of MedicinesShenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhenChina
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Yao YL, Ma XY, Wang TY, Yan JY, Chen NF, Hong JS, Liu BQ, Xu ZQ, Zhang N, Lv C, Sun X, Luan JB. A bacteriocyte symbiont determines whitefly sex ratio by regulating mitochondrial function. Cell Rep 2023; 42:112102. [PMID: 36774548 DOI: 10.1016/j.celrep.2023.112102] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 02/13/2023] Open
Abstract
Nutritional symbionts influence host reproduction, but the underlying molecular mechanisms are largely unclear. We previously found that the bacteriocyte symbiont Hamiltonella impacts the sex ratio of the whitefly Bemisia tabaci. Hamiltonella synthesizes folate by cooperation with the whitefly. Folate deficiency by Hamiltonella elimination or whitefly gene silencing distorted whitefly sex ratio, and folate supplementation restored the sex ratio. Hamiltonella deficiency or gene silencing altered histone H3 lysine 9 trimethylation (H3K9me3) level, which was restored by folate supplementation. Genome-wide chromatin immunoprecipitation-seq analysis of H3K9me3 indicated mitochondrial dysfunction in symbiont-deficient whiteflies. Hamiltonella deficiency compromised mitochondrial quality of whitefly ovaries. Repressing ovary mitochondrial function led to distorted whitefly sex ratio. These findings indicate that the symbiont-derived folate regulates host histone methylation modifications, which thereby impacts ovary mitochondrial function, and finally determines host sex ratio. Our study suggests that a nutritional symbiont can regulate animal reproduction in a way that differs from reproductive manipulators.
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Affiliation(s)
- Ya-Lin Yao
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xin-Yu Ma
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tian-Yu Wang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jin-Yang Yan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nai-Fei Chen
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Ji-Sheng Hong
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing-Qi Liu
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zi-Qi Xu
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nuo Zhang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chao Lv
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiang Sun
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jun-Bo Luan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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Teruya T, Sunagawa S, Mori A, Masuzaki H, Yanagida M. Markers for obese and non-obese Type 2 diabetes identified using whole blood metabolomics. Sci Rep 2023; 13:2460. [PMID: 36774491 PMCID: PMC9922320 DOI: 10.1038/s41598-023-29619-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/07/2023] [Indexed: 02/13/2023] Open
Abstract
Definitive differences in blood metabolite profiles between obese and non-obese Type 2 diabetes (T2D) have not been established. We performed an LC-MS-based non-targeted metabolomic analysis of whole blood samples collected from subjects classified into 4 types, based on the presence or absence of obesity and T2D. Of the 125 compounds identified, 20, comprising mainly nucleobases and glucose metabolites, showed significant increases or decreases in the T2D group. These included cytidine, UDP-glucuronate, UMP, 6-phosphogluconate, and pentose-phosphate. Among those 20 compounds, 11 enriched in red blood cells (RBCs) have rarely been studied in the context of diabetes, indicating that RBC metabolism is more extensively disrupted than previously known. Correlation analysis revealed that these T2D markers include 15 HbA1c-associated and 5 irrelevant compounds that may reflect diabetic conditions by a different mechanism than that of HbA1c. In the obese group, enhanced protein and fatty acid catabolism causes increases in 13 compounds, including methylated or acetylated amino acids and short-chain carnitines. Our study, which may be considered a pilot investigation, suggests that changes in blood metabolism due to obesity and diabetes are large, but essentially independent.
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Affiliation(s)
- Takayuki Teruya
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
- R&D Cluster Programs Section, Technology Development and Innovation Center, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Sumito Sunagawa
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology (Second Department of Internal Medicine), Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Ayaka Mori
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
- Cell Division Dynamics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Hiroaki Masuzaki
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology (Second Department of Internal Medicine), Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan.
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8
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Jongkhumkrong J, Thaveesangsakulthai I, Sukbangnop W, Kulsing C, Sooksimuang T, Aonbangkhen C, Sahasithiwat S, Sriprasart T, Palaga T, Chantaravisoot N, Tomapatanaget B. Helicene-Hydrazide Encapsulated Ethyl Cellulose as a Potential Fluorescence Sensor for Highly Specific Detection of Nonanal in Aqueous Solutions and a Proof-of-Concept Clinical Study in Lung Fluid. ACS APPLIED MATERIALS & INTERFACES 2022; 14:49495-49507. [PMID: 36301188 DOI: 10.1021/acsami.2c11064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Over the past years, lung cancer has been one of the vital cancer-related mortalities worldwide and has inevitably exhibited the highest death rate with the subsequent need for facile and convenient diagnosis approaches to identify the severity of cancer. Previous research has reported long-chain aldehyde compounds such as hexanal, heptanal, octanal, and nonanal as potential biomarkers of lung cancer. Herein, the helicene dye-encapsulated ethyl cellulose (EC@dye-NH) nanosensors have been applied for the potentially sensitive and specific detection of long-chain aldehydes in aqueous media. The sensors contain the intrinsic hydrazide group of dye-NH, which is capable of reacting an aldehyde group via imine formation and the EC backbone. This offers the synergistic forces of hydrophobic interactions with alkyl long-chain aldehydes, which could induce self-assembly encapsulation of EC@dye-NH nanosensors and strong fluorescence responses. The addition of long-chain aldehyde would induce the complete micellar-like nanoparticle formation within 15 min in acetate buffer pH 5.0. The limit of detection (LOD) values of EC@dye-NH nanosensors toward heptanal, octanal, and nonanal were 40, 100, and 10 μM, respectively, without interference from the lung fluid matrices and short-chain aldehydes. For practical applicability, this sensing platform was developed for quantification of the long-chain aldehydes in lung fluid samples with 98-101% recoveries. This EC@dye-NH nanosensor was applied to quantify nonanal contents in lung fluid samples. The results of this method based on EC@dye-NH nanosensors were then validated using standard gas chromatography-mass spectrometry (GC-MS), which gave results consistent with the proposed method. With intracellular imaging application, the EC@dye-NH nanosensors demonstrated excellent intracellular uptake and strong green fluorescence emission upon introducing the nonanal into the lung cancer cells (A549). Thus, the developed nanosensing approach served as the potential fluorescent probes in medical and biological fields, especially for lung cancer disease diagnosis based on highly selective and sensitive detection of long-chain aldehydes.
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Affiliation(s)
- Jinnawat Jongkhumkrong
- Supramolecular Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | | | - Wannee Sukbangnop
- National Metal and Materials Technology Center (MTEC), National Science and Technology Development Agency (NSTDA), 114 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani12120, Thailand
| | - Chadin Kulsing
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Thanasat Sooksimuang
- National Metal and Materials Technology Center (MTEC), National Science and Technology Development Agency (NSTDA), 114 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani12120, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Somboon Sahasithiwat
- National Metal and Materials Technology Center (MTEC), National Science and Technology Development Agency (NSTDA), 114 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani12120, Thailand
| | - Thitiwat Sriprasart
- Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok10330, Thailand
| | - Tanapat Palaga
- Center of Excellence in Materials and Bio-interfaces, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Naphat Chantaravisoot
- Department of Biochemistry, Chulalongkorn University Faculty of Medicine, Bangkok10330, Thailand
| | - Boosayarat Tomapatanaget
- Supramolecular Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
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9
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Tzanakis K, Nattkemper TW, Niehaus K, Albaum SP. MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data. BMC Bioinformatics 2022; 23:267. [PMID: 35804309 PMCID: PMC9270834 DOI: 10.1186/s12859-022-04793-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Modern mass spectrometry has revolutionized the detection and analysis of metabolites but likewise, let the data skyrocket with repositories for metabolomics data filling up with thousands of datasets. While there are many software tools for the analysis of individual experiments with a few to dozens of chromatograms, we see a demand for a contemporary software solution capable of processing and analyzing hundreds or even thousands of experiments in an integrative manner with standardized workflows. RESULTS Here, we introduce MetHoS as an automated web-based software platform for the processing, storage and analysis of great amounts of mass spectrometry-based metabolomics data sets originating from different metabolomics studies. MetHoS is based on Big Data frameworks to enable parallel processing, distributed storage and distributed analysis of even larger data sets across clusters of computers in a highly scalable manner. It has been designed to allow the processing and analysis of any amount of experiments and samples in an integrative manner. In order to demonstrate the capabilities of MetHoS, thousands of experiments were downloaded from the MetaboLights database and used to perform a large-scale processing, storage and statistical analysis in a proof-of-concept study. CONCLUSIONS MetHoS is suitable for large-scale processing, storage and analysis of metabolomics data aiming at untargeted metabolomic analyses. It is freely available at: https://methos.cebitec.uni-bielefeld.de/ . Users interested in analyzing their own data are encouraged to apply for an account.
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Affiliation(s)
- Konstantinos Tzanakis
- International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| | - Tim W Nattkemper
- Biodata Mining Group, Center for Biotechnology (CeBiTec), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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10
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Lanznaster D, Bruno C, Bourgeais J, Emond P, Zemmoura I, Lefèvre A, Reynier P, Eymieux S, Blanchard E, Vourc’h P, Andres CR, Bakkouche SE, Herault O, Favard L, Corcia P, Blasco H. Metabolic Profile and Pathological Alterations in the Muscle of Patients with Early-Stage Amyotrophic Lateral Sclerosis. Biomedicines 2022; 10:biomedicines10061307. [PMID: 35740329 PMCID: PMC9220134 DOI: 10.3390/biomedicines10061307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 12/26/2022] Open
Abstract
Diverse biomarkers and pathological alterations have been found in muscle of patients with Amyotrophic lateral sclerosis (ALS), but the relation between such alterations and dysfunction in energetic metabolism remains to be investigated. We established the metabolome of muscle and serum of ALS patients and correlated these findings with the clinical status and pathological alterations observed in the muscle. We obtained data from 20 controls and 17 ALS patients (disease duration: 9.4 ± 6.8 months). Multivariate metabolomics analysis identified a distinct serum metabolome for ALS compared to controls (p-CV-ANOVA < 0.035) and revealed an excellent discriminant profile for muscle metabolome (p-CV-ANOVA < 0.0012). Citramalate was discriminant for both muscle and serum. High lauroylcarnitine levels in muscle were associated with low Forced Vital Capacity. Transcriptomics analysis of key antioxidant enzymes showed an upregulation of SOD3 (p = 0.0017) and GLRX2(1) (p = 0.0022) in ALS muscle. Analysis of mitochondrial enzymatic activity in muscle revealed higher complex II/CS (p = 0.04) and lower LDH (p = 0.03) activity in ALS than in controls. Our study showed, for the first time, a global dysfunction in the muscle of early-stage ALS patients. Furthermore, we identified novel metabolites to be employed as biomarkers for diagnosis and prognosis of ALS patients.
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Affiliation(s)
- Débora Lanznaster
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Correspondence:
| | - Clément Bruno
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
| | - Jérôme Bourgeais
- CNRS ERL7001, EA 7501 GICC, Université de Tours, 37000 Tours, France; (J.B.); (O.H.)
| | - Patrick Emond
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Médecine Nucléaire In Vitro, CHU de Tours, 37000 Tours, France
| | - Ilyess Zemmoura
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Neurochirurgie, CHU de Tours, 37000 Tours, France
| | - Antoine Lefèvre
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
| | - Pascal Reynier
- Service de Biochimie et Biologie Moléculaire, CHU d’Angers, 49000 Angers, France;
- Mitovasc-Mitolab, UMR CNRS6015-INSERM1083, 49000 Angers, France
| | - Sébastien Eymieux
- Plateforme IBiSA de Microscopie Electronique, Université de Tours et CHU de Tours, 37000 Tours, France; (S.E.); (E.B.)
- INSERM U1259, Université de Tours, 37000 Tours, France
| | - Emmanuelle Blanchard
- Plateforme IBiSA de Microscopie Electronique, Université de Tours et CHU de Tours, 37000 Tours, France; (S.E.); (E.B.)
- INSERM U1259, Université de Tours, 37000 Tours, France
| | - Patrick Vourc’h
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
| | - Christian R. Andres
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
| | | | - Olivier Herault
- CNRS ERL7001, EA 7501 GICC, Université de Tours, 37000 Tours, France; (J.B.); (O.H.)
| | - Luc Favard
- Service de Neurologie, CHU de Tours, 37000 Tours, France;
| | - Philippe Corcia
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Neurologie, CHU de Tours, 37000 Tours, France;
| | - Hélène Blasco
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
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11
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Eilertz D, Mitterer M, Buescher JM. automRm: An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning. Anal Chem 2022; 94:6163-6171. [PMID: 35412809 PMCID: PMC9047440 DOI: 10.1021/acs.analchem.1c05224] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Preprocessing of liquid chromatography-mass spectrometry (LC-MS) raw data facilitates downstream statistical and biological data analyses. In the case of targeted LC-MS data, consistent recognition of chromatographic peaks is a main challenge, in particular, for low abundant signals. Fully automatic preprocessing is faster than manual peak review and does not depend on the individual operator. Here, we present the R package automRm for fully automatic preprocessing of LC-MS data recorded in MRM mode. Using machine learning (ML) for detection of chromatographic peaks and quality control of reported results enables the automatic recognition of complex patterns in raw data. In addition, this approach renders automRm generally applicable to a wide range of analytical methods including hydrophilic interaction liquid chromatography (HILIC), which is known for sample-to-sample variations in peak shape and retention time. We demonstrate the impact of the choice of training data set, of the applied ML algorithm, and of individual peak characteristics on automRm's ability to correctly report chromatographic peaks. Next, we show that automRm can replicate results obtained by manual peak review on published data. Moreover, automRm outperforms alternative software solutions regarding the variation in peak integration among replicate measurements and the number of correctly reported peaks when applied to a HILIC-MS data set. The R package is freely available from gitlab (https://gitlab.gwdg.de/joerg.buescher/automrm).
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Affiliation(s)
- Daniel Eilertz
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Michael Mitterer
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Joerg M Buescher
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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12
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Kondoh H, Teruya T, Kameda M, Yanagida M. Decline of ergothioneine in frailty and cognition impairment. FEBS Lett 2022; 596:1270-1278. [PMID: 35090053 DOI: 10.1002/1873-3468.14299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/08/2022]
Abstract
Ergothioneine is a well-known anti-oxidant that is abundant in both human red blood cells and in fission yeast responding to nutritional stress. In frail elderly people, whose aging organs undergo functional decline, there is a correlation between ergothioneine levels and cognitive, but not skeletal muscle decline. In patients suffering from dementia, including Alzheimer's disease with hippocampal atrophy, deteriorating cognitive ability is correlated with declining ergothioneine levels. S-methyl-ergothioneine, trimethyl-histidine, and three other trimethyl-ammonium compounds also decrease sharply in dementia, whereas compounds such as indoxyl-sulfate and quinolinic acid increase, possibly exacerbating the disease. Using these opposing dementia markers, not only diagnosis, but also therapeutic interventions to mitigate cognitive decline may now become possible.
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Affiliation(s)
- Hiroshi Kondoh
- Geriatric unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Teruya
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Masahiro Kameda
- Geriatric unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
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13
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Whole-blood metabolomics of dementia patients reveal classes of disease-linked metabolites. Proc Natl Acad Sci U S A 2021; 118:2022857118. [PMID: 34493657 PMCID: PMC8449400 DOI: 10.1073/pnas.2022857118] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/08/2021] [Indexed: 01/03/2023] Open
Abstract
Dementia is a slowly progressing, chronic, and usually irreversible decline in cognitive function. Mechanistic causes and definitive treatments remain elusive. Using comprehensive metabolomics, we identified five groups of 33 metabolites (A to E), 13 of them previously reported, possibly useful for diagnosis and therapy of forms of dementia, such as Alzheimer’s disease. Seven A compounds may act as neurotoxins, whereas B to E compounds may protect the nervous system against oxidative stress, maintain energy reserves, supply nutrients and neuroprotective factors. Five metabolites, ergothioneine, S-methyl-ergothioneine, trimethyl-histidine, methionine, and tryptophan, overlap with those reported for frailty. Interventions for cognitive diseases involving these dementia metabolomic markers may be accomplished either by inhibiting A compounds or by supplementing B to E compounds in patients. Dementia is caused by factors that damage neurons. We quantified small molecular markers in whole blood of dementia patients, using nontargeted liquid chromatography–mass spectroscopy (LC-MS). Thirty-three metabolites, classified into five groups (A to E), differed significantly in dementia patients, compared with healthy elderly subjects. Seven A metabolites present in plasma, including quinolinic acid, kynurenine, and indoxyl-sulfate, increased. Possibly they act as neurotoxins in the central nervous system (CNS). The remaining 26 compounds (B to E) decreased, possibly causing a loss of support or protection of the brain in dementia. Six B metabolites, normally enriched in red blood cells (RBCs), all contain trimethylated ammonium moieties. These metabolites include ergothioneine and structurally related compounds that have scarcely been investigated as dementia markers, validating the examination of RBC metabolites. Ergothioneine, a potent antioxidant, is significantly decreased in various cognition-related disorders, such as mild cognitive impairment and frailty. C compounds also include some oxidoreductants and are normally abundant in RBCs (NADP+, glutathione, adenosine triphosphate, pantothenate, S-adenosyl-methionine, and gluconate). Their decreased levels in dementia patients may also contribute to depressed brain function. Twelve D metabolites contains plasma compounds, such as amino acids, glycerophosphocholine, dodecanoyl-carnitine, and 2-hydroxybutyrate, which normally protect the brain, but their diminution in dementia may reduce that protection. Seven D compounds have been identified previously as dementia markers. B to E compounds may be critical to maintain the CNS by acting directly or indirectly. How RBC metabolites act in the CNS and why they diminish significantly in dementia remain to be determined.
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14
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Human age-declined saliva metabolic markers determined by LC-MS. Sci Rep 2021; 11:18135. [PMID: 34518599 PMCID: PMC8437986 DOI: 10.1038/s41598-021-97623-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/26/2021] [Indexed: 01/20/2023] Open
Abstract
Metabolites in human biofluids reflect individual physiological states influenced by various factors. Using liquid chromatography-mass spectrometry (LC–MS), we conducted non-targeted, non-invasive metabolomics using saliva of 27 healthy volunteers in Okinawa, comprising 13 young (30 ± 3 year) and 14 elderly (76 ± 4 year) subjects. Few studies have comprehensively identified age-dependent changes in salivary metabolites. Among 99 salivary metabolites, 21 were statistically age-related. All of the latter decline in abundance with advancing age, except ATP, which increased 1.96-fold in the elderly, possibly due to reduced ATP consumption. Fourteen age-linked and highly correlated compounds function in a metabolic network involving the pentose-phosphate pathway, glycolysis/gluconeogenesis, amino acids, and purines/pyrimidines nucleobases. The remaining seven less strongly correlated metabolites, include ATP, anti-oxidation-related glutathione disulfide, muscle-related acetyl-carnosine, N-methyl-histidine, creatinine, RNA-related dimethyl-xanthine and N-methyl-adenosine. In addition, glutamate and N-methyl-histidine are related to taste, so their decline suggests that the elderly lose some ability to taste. Reduced redox metabolism and muscle activity are suggested by changes in glutathione and acetyl-carnosine. These age-linked salivary metabolites together illuminate a metabolic network that reflects a decline of oral functions during human aging.
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15
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亀田 雅, 近藤 祥. [Metabolites for frailty biomarkers]. Nihon Ronen Igakkai Zasshi 2021; 58:333-340. [PMID: 34483155 DOI: 10.3143/geriatrics.58.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Reduced uremic metabolites are prominent feature of sarcopenia, distinct from antioxidative markers for frailty. Aging (Albany NY) 2021; 13:20915-20934. [PMID: 34492634 PMCID: PMC8457568 DOI: 10.18632/aging.203498] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Due to global aging, frailty and sarcopenia are increasing. Sarcopenia is defined as loss of volume and strength of skeletal muscle in elderlies, while frailty involves multiple domains of aging-related dysfunction, impaired cognition, hypomobility, and decreased social activity. However, little is known about the metabolic basis of sarcopenia, either shared with or discrete from frailty. Here we analyzed comprehensive metabolomic data of human blood in relation to sarcopenia, previously collected from 19 elderly participants in our frailty study. Among 131 metabolites, we identified 22 sarcopenia markers, distinct from 15 frailty markers, mainly including antioxidants, although sarcopenia overlaps clinically with physical frailty. Notably, 21 metabolites that decline in sarcopenia or low SMI are uremic compounds that increase in kidney dysfunction. These comprise TCA cycle, urea cycle, nitrogen, and methylated metabolites. Sarcopenia markers imply a close link between muscle and kidney function, while frailty markers define a state vulnerable to oxidative stress.
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17
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Analytical considerations for reducing the matrix effect for the sphingolipidome quantification in whole blood. Bioanalysis 2021; 13:1037-1049. [PMID: 34110924 PMCID: PMC8240607 DOI: 10.4155/bio-2021-0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Aim: Plasma and serum are widely used blood-derived biofluids for metabolomics and lipidomics assays, but analytes that are present in high concentrations in blood cells cannot be evaluated in those samples and isolating serum or plasma could introduce additional variability in the data. Materials & methods: In this study, we provide a comprehensive method for quantification of the whole blood (WB) sphingolipidome, combining a single-phase extraction method with LC-high-resolution mass spectrometry. Results: We were able to quantify more than 150 sphingolipids, and when compared with paired plasma, WB contained higher concentration of most sphingolipids and individual variations were lower. These findings suggest that WB could be a better alternative to plasma, and potentially guide the evaluation of the sphingolipidome for biomarker discovery.
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18
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Whole Blood Metabolomics in Aging Research. Int J Mol Sci 2020; 22:ijms22010175. [PMID: 33375345 PMCID: PMC7796096 DOI: 10.3390/ijms22010175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/25/2020] [Accepted: 12/25/2020] [Indexed: 02/08/2023] Open
Abstract
Diversity is observed in the wave of global aging because it is a complex biological process exhibiting individual variability. To assess aging physiologically, markers for biological aging are required in addition to the calendar age. From a metabolic perspective, the aging hypothesis includes the mitochondrial hypothesis and the calorie restriction (CR) hypothesis. In experimental models, several compounds or metabolites exert similar lifespan-extending effects, like CR. However, little is known about whether these metabolic modulations are applicable to human longevity, as human aging is greatly affected by a variety of factors, including lifestyle, genetic or epigenetic factors, exposure to stress, diet, and social environment. A comprehensive analysis of the human blood metabolome captures complex changes with individual differences. Moreover, a non-targeted analysis of the whole blood metabolome discloses unexpected aspects of human biology. By using such approaches, markers for aging or aging-relevant conditions were identified. This information should prove valuable for future diagnosis or clinical interventions in diseases relevant to aging.
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19
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Borodina I, Kenny LC, McCarthy CM, Paramasivan K, Pretorius E, Roberts TJ, van der Hoek SA, Kell DB. The biology of ergothioneine, an antioxidant nutraceutical. Nutr Res Rev 2020; 33:190-217. [PMID: 32051057 PMCID: PMC7653990 DOI: 10.1017/s0954422419000301] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023]
Abstract
Ergothioneine (ERG) is an unusual thio-histidine betaine amino acid that has potent antioxidant activities. It is synthesised by a variety of microbes, especially fungi (including in mushroom fruiting bodies) and actinobacteria, but is not synthesised by plants and animals who acquire it via the soil and their diet, respectively. Animals have evolved a highly selective transporter for it, known as solute carrier family 22, member 4 (SLC22A4) in humans, signifying its importance, and ERG may even have the status of a vitamin. ERG accumulates differentially in various tissues, according to their expression of SLC22A4, favouring those such as erythrocytes that may be subject to oxidative stress. Mushroom or ERG consumption seems to provide significant prevention against oxidative stress in a large variety of systems. ERG seems to have strong cytoprotective status, and its concentration is lowered in a number of chronic inflammatory diseases. It has been passed as safe by regulatory agencies, and may have value as a nutraceutical and antioxidant more generally.
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Affiliation(s)
- Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
| | - Louise C. Kenny
- Department of Women’s and Children’s Health, Institute of Translational Medicine, University of Liverpool, Crown Street, LiverpoolL8 7SS, UK
| | - Cathal M. McCarthy
- Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork University Maternity Hospital, Cork, Republic of Ireland
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, Cork, Republic of Ireland
| | - Kalaivani Paramasivan
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Timothy J. Roberts
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, LiverpoolL69 7ZB, UK
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, LiverpoolL69 7ZB, UK
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20
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Teruya T, Goga H, Yanagida M. Aging markers in human urine: A comprehensive, non-targeted LC-MS study. FASEB Bioadv 2020; 2:720-733. [PMID: 33336159 PMCID: PMC7734427 DOI: 10.1096/fba.2020-00047] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/04/2020] [Accepted: 09/28/2020] [Indexed: 12/25/2022] Open
Abstract
Metabolites in human biofluids document the physiological status of individuals. We conducted comprehensive, non-targeted, non-invasive metabolomic analysis of urine from 27 healthy human subjects, comprising 13 young adults (30 ± 3 years) and 14 seniors (76 ± 4 years). Quantitative analysis of 99 metabolites revealed 55 that displayed significant differences in abundance between the two groups. Forty-four did not show a statistically significant relationship with age. These include 13 standard amino acids, 5 methylated, 4 acetylated, and 9 other amino acids, 6 nucleosides, nucleobases, and derivatives, 4 sugar derivatives, 5 sugar phosphates, 4 carnitines, 2 hydroxybutyrates, 1 choline, and 1 ethanolamine derivative, and glutathione disulfide. Abundances of 53 compounds decreased, while 2 (glutathione disulfide, myo-inositol) increased in elderly people. The great majority of age-linked markers were highly correlated with creatinine. In contrast, 44 other urinary metabolites, including urate, carnitine, hippurate, and betaine, were not age-linked, neither declining nor increasing in elderly subjects. As metabolite profiles of urine and blood are quite different, age-related information in urine offers additional valuable insights into aging mechanisms of endocrine system. Correlation analysis of urinary metabolites revealed distinctly inter-related groups of compounds.
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Affiliation(s)
- Takayuki Teruya
- G0 Cell UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Haruhisa Goga
- G0 Cell UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
- Forensic Laboratory, Department of Criminal InvestigationOkinawa Prefectural Police HQOkinawaJapan
| | - Mitsuhiro Yanagida
- G0 Cell UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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21
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Abstract
Since ancient days, human fasting has been performed for religious or political reasons. More recently, fasting has been employed as an effective therapy for weight reduction by obese people, and numerous studies have investigated the physiology of fasting by obese subjects. Well-established fasting markers (butyrates, BCAAs and carnitines) were considered essential energy substitutes after glycogen storage depletion. However, a recently developed metabolomic approach has unravelled previously unappreciated aspects of fasting. Surprisingly, one-third (44) of 120 metabolites investigated increase during 58 h of fasting, including antioxidative metabolites (carnosine, ophthalmic acid, ergothioneine and urates) and metabolites of entire pathways, such as the pentose phosphate pathway. Signalling metabolites (3-hydroxybutyrate and 2-oxoglutarate) and purines/pyrimidines may also serve as transcriptional modulators. Thus, prolonged fasting activates both global catabolism and anabolism, reprogramming metabolic homeostasis.
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Affiliation(s)
- Hiroshi Kondoh
- Geriatric unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Teruya
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
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22
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Wang T, Sun Z, Wang Y, Li F, Zhou X, Tian X, Wang S. Diagnosis of papillary thyroid carcinoma by 1H NMR spectroscopy-based metabolomic analysis of whole blood. Drug Discov Ther 2020; 14:187-196. [PMID: 32848112 DOI: 10.5582/ddt.2020.03062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The incidence rate of thyroid carcinoma, especially papillary thyroid carcinoma (PTC), has increased significantly over time. As a primary pathway for metastasis, the lymphatic system is an important prognostic factor for PTC patients. Although the metabolic changes in PTC patients have been investigated in extensive studies, few studies focused on the whole blood metabolic profiling of PTC patients. In this study, we investigated the 1H NMR-based metabolic profiles of whole blood samples that were obtained from healthy individuals and PTC patients, with or without lymph node metastasis. The estimation of the predictive potential of metabolites was evaluated using multivariate statistical analyses, which revealed that the whole blood carries information that is sufficient for distinguishing between PTC patients and healthy individuals. However, PTC patients were not well classified as positive or negative according to the lymph nodes. We did not find a metabolite that could discriminate the presence of lymph node metastasis. Further studies with larger sample sizes are needed to elucidate significant metabolites to indicate the presence of lymph node metastasis in patients with PTC.
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Affiliation(s)
- Tiantian Wang
- School of Pharmaceutical Sciences, Shandong University, Ji'nan, Shandong, China.,Department of Thyroid and Breast Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong, China
| | - Zhigang Sun
- Department of Thyroid and Breast Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong, China.,Department of Colorectal Surgery and State Key Lab of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Wang
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University College of Medicine, Hangzhou, Zhejiang, China
| | - Feifei Li
- School of Pharmaceutical Sciences, Shandong University, Ji'nan, Shandong, China
| | - Xiaoming Zhou
- Department of Thyroid and Breast Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong, China
| | - Xingsong Tian
- Department of Thyroid and Breast Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong, China
| | - Shuqi Wang
- School of Pharmaceutical Sciences, Shandong University, Ji'nan, Shandong, China
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23
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Frailty markers comprise blood metabolites involved in antioxidation, cognition, and mobility. Proc Natl Acad Sci U S A 2020; 117:9483-9489. [PMID: 32295884 PMCID: PMC7196897 DOI: 10.1073/pnas.1920795117] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Frailty resulting from age-related deterioration of multiple organ systems displays complex features, including cognitive dysfunction, hypomobility, and impaired daily activity. However, metabolic aspects of frailty remain unclear. We performed untargeted, comprehensive metabolomics of whole blood from 19 frail and nonfrail elderly patients. We identified 22 markers, including 15 for frailty, 6 for cognition, and 12 for hypomobility, most of which are abundant in blood. Frailty markers include 5 of 6 for cognition and 6 of 12 for hypomobility. These overlapping markers include decreased levels of metabolites related to antioxidation, nitrogen, and amino acid metabolism. Ergothioneine, an antioxidant involved in neuronal diseases, declines in frailty. Thus, we reveal essential metabolites linked to the pathogenesis of frailty, including vulnerability to oxidative stress. As human society ages globally, age-related disorders are becoming increasingly common. Due to decreasing physiological reserves and increasing organ system dysfunction associated with age, frailty affects many elderly people, compromising their ability to cope with acute stressors. Frail elderly people commonly manifest complex clinical symptoms, including cognitive dysfunction, hypomobility, and impaired daily activity, the metabolic basis of which remains poorly understood. We applied untargeted, comprehensive LC-MS metabolomic analysis to human blood from 19 frail and nonfrail elderly patients who were clinically evaluated using the Edmonton Frail Scale, the MoCA-J for cognition, and the TUG for mobility. Among 131 metabolites assayed, we identified 22 markers for frailty, cognition, and hypomobility, most of which were abundant in blood. Frailty markers included 5 of 6 markers specifically related to cognition and 6 of 12 markers associated with hypomobility. These overlapping sets of markers included metabolites related to antioxidation, muscle or nitrogen metabolism, and amino acids, most of which are decreased in frail elderly people. Five frailty-related metabolites that decreased—1,5-anhydroglucitol, acetyl-carnosine, ophthalmic acid, leucine, and isoleucine—have been previously reported as markers of aging, providing a metabolic link between human aging and frailty. Our findings clearly indicate that metabolite profiles efficiently distinguish frailty from nonfrailty. Importantly, the antioxidant ergothioneine, which decreases in frailty, is neuroprotective. Oxidative stress resulting from diminished antioxidant levels could be a key vulnerability for the pathogenesis of frailty, exacerbating illnesses related to human aging.
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24
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Tominaga A, Higuchi Y, Mori H, Akai M, Suyama A, Yamada N, Takegawa K. Catechol O-methyltransferase homologs in Schizosaccharomyces pombe are response factors to alkaline and salt stress. Appl Microbiol Biotechnol 2019; 103:4881-4887. [PMID: 31053915 DOI: 10.1007/s00253-019-09858-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/28/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
How cells of the fission yeast Schizosaccharomyces pombe respond to alkaline stress is not well understood. Here, to elucidate the molecular mechanism underlying the alkaline stress response in S. pombe, we performed DNA microarray analysis. We found that a homolog of human catechol O-methyltransferase 2 (COMT2) is highly upregulated in S. pombe cells exposed to alkaline conditions. We designated the S. pombe homolog as cmt2+ and also identified its paralog, cmt1+, in the S. pombe genome. Reverse transcription PCR confirmed that both cmt1+ and cmt2+ are upregulated within 1 h of exposure to alkaline stress and downregulated within 30 min of returning to an acidic environment. Moreover, we verified that recombinant Cmt proteins exhibit catechol O-methyltransferase activity. To further characterize the expression of cmt1+ and cmt2+, we carried out an EGFP reporter assay using their promoter sequences, which showed that both genes respond not only to alkaline but also to salt stress. Collectively, our findings indicate that the cmt promoter might be an advantageous expression system for use in S. pombe under alkaline culture conditions.
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Affiliation(s)
- Akihiro Tominaga
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hikari Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Makoto Akai
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Akiko Suyama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Naotaka Yamada
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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25
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Diverse metabolic reactions activated during 58-hr fasting are revealed by non-targeted metabolomic analysis of human blood. Sci Rep 2019; 9:854. [PMID: 30696848 PMCID: PMC6351603 DOI: 10.1038/s41598-018-36674-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022] Open
Abstract
During human fasting, metabolic markers, including butyrates, carnitines, and branched-chain amino acids, are upregulated for energy substitution through gluconeogenesis and use of stored lipids. We performed non-targeted, accurate semiquantitative metabolomic analysis of human whole blood, plasma, and red blood cells during 34–58 hr fasting of four volunteers. During this period, 44 of ~130 metabolites increased 1.5~60-fold. Consistently fourteen were previously reported. However, we identified another 30 elevated metabolites, implicating hitherto unrecognized metabolic mechanisms induced by fasting. Metabolites in pentose phosphate pathway are abundant, probably due to demand for antioxidants, NADPH, gluconeogenesis and anabolic metabolism. Global increases of TCA cycle-related compounds reflect enhanced mitochondrial activity in tissues during fasting. Enhanced purine/pyrimidine metabolites support RNA/protein synthesis and transcriptional reprogramming, which is promoted also by some fasting-related metabolites, possibly via epigenetic modulations. Thus diverse, pronounced metabolite increases result from greatly activated catabolism and anabolism stimulated by fasting. Anti-oxidation may be a principal response to fasting.
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26
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Nagana Gowda GA, Raftery D. Analysis of Plasma, Serum, and Whole Blood Metabolites Using 1H NMR Spectroscopy. Methods Mol Biol 2019; 2037:17-34. [PMID: 31463837 DOI: 10.1007/978-1-4939-9690-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Blood is the most widely used biological specimen in the metabolomics field. With its unique characteristics of high reproducibility and excellent quantitation, NMR spectroscopy offers immense benefits for the analysis of blood metabolites. In the metabolomics field, intact blood serum and plasma have been widely used for many years. However, such analysis has met with challenges arising from the deleterious effects of the abundant proteins in serum and plasma. Recent advances have led to the development of improved NMR methods that involve removal of protein before analysis. In particular, protein removal by precipitation using methanol alone or using a mixture of methanol and chloroform was shown to be an optimal method for metabolite recovery and for producing highly resolved NMR spectra. This has led to the absolute quantitation of nearly 70 metabolites in serum and plasma and nearly 80 in whole blood. In this chapter, we describe protocols for the analysis of blood serum, blood plasma, and whole blood metabolites using 1D 1H NMR spectroscopy methods.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.,Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.,Mitochondria and Metabolism Center, University of Washington, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA. .,Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA. .,Mitochondria and Metabolism Center, University of Washington, Seattle, WA, USA. .,Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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27
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Chaleckis R, Ohashi K, Meister I, Naz S, Wheelock CE. Metabolomic Analysis of Yeast and Human Cells: Latest Advances and Challenges. Methods Mol Biol 2019; 2049:233-245. [PMID: 31602615 DOI: 10.1007/978-1-4939-9736-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) based nontargeted metabolomics has been applied to a wide range of biological samples and can provide information on thousands of compounds. However, reliable identification of the compounds remains a challenge affecting result interpretation. In this protocol, we describe comparable yeast cell and whole blood metabolome sample preparation for extracting similar compound groups, and we present a LC-MS method using the all ion fragmentation (AIF) approach for the purposes of increasing accuracy in metabolite annotation. Our method enables database-dependent targeted as well as nontargeted metabolomics analysis from the same data acquisition, while simultaneously improving the accuracy in metabolite identification to increase the quality of the resulting biological information.
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Affiliation(s)
- Romanas Chaleckis
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Kazuto Ohashi
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Isabel Meister
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Shama Naz
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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28
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Chaleckis R, Meister I, Zhang P, Wheelock CE. Challenges, progress and promises of metabolite annotation for LC-MS-based metabolomics. Curr Opin Biotechnol 2018; 55:44-50. [PMID: 30138778 DOI: 10.1016/j.copbio.2018.07.010] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
Abstract
Accurate annotation is vital for data interpretation; however, metabolite identification is a major bottleneck in untargeted metabolomics. Although community guidelines for metabolite identification were published over a decade ago, adaptation of the recommended standards has been limited. The complexity of LC-MS data due to combinations of various chromatographic and mass spectrometric acquisition methods has resulted in the advent of diverse workflows, which often involve non-standardized manual curation. Herein, we review the parameters involved in metabolite reporting and provide a workflow to estimate the level of confidence in reported metabolite annotation. The future of metabolite identification will be heavily based upon the use of metabolome data repositories and associated data analysis tools, which will enable data to be shared, re-analyzed and re-annotated in an automated fashion.
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Affiliation(s)
- Romanas Chaleckis
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Meister
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pei Zhang
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma, Japan; Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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29
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Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL. The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut. Cell Host Microbe 2018; 24:120-132.e6. [PMID: 30008292 PMCID: PMC6086485 DOI: 10.1016/j.chom.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/21/2018] [Accepted: 06/05/2018] [Indexed: 01/16/2023]
Abstract
In the mammalian gut, bacteria compete for resources to maintain their populations, but the factors determining their success are poorly understood. We report that the human gut bacterium Bacteroides thetaiotaomicron relies on the stringent response, an intracellular signaling pathway that allocates resources away from growth, to survive carbon starvation and persist in the gut. Genome-scale transcriptomics, 13C-labeling, and metabolomics analyses reveal that B. thetaiotaomicron uses the alarmone (p)ppGpp to repress multiple biosynthetic pathways and upregulate tricarboxylic acid (TCA) cycle genes in these conditions. During carbon starvation, (p)ppGpp triggers accumulation of the metabolite alpha-ketoglutarate, which itself acts as a metabolic regulator; alpha-ketoglutarate supplementation restores viability to a (p)ppGpp-deficient strain. These studies uncover how commensal bacteria adapt to the gut by modulating central metabolism and reveal that halting rather than accelerating growth can be a determining factor for membership in the gut microbiome.
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Affiliation(s)
- Whitman B Schofield
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Maria Zimmermann-Kogadeeva
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Natasha A Barry
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
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30
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Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW. Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics. ACS Chem Biol 2018; 13:1029-1037. [PMID: 29510029 DOI: 10.1021/acschembio.7b01089] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Natural products (NPs) are a rich source of medicines, but traditional discovery methods are often unsuccessful due to high rates of rediscovery. Genetic approaches for NP discovery are promising, but progress has been slow due to the difficulty of identifying unique biosynthetic gene clusters (BGCs) and poor gene expression. We previously developed the metabologenomics method, which combines genomic and metabolomic data to discover new NPs and their BGCs. Here, we utilize metabologenomics in combination with molecular networking to discover a novel class of NPs, the tyrobetaines: nonribosomal peptides with an unusual trimethylammonium tyrosine residue. The BGC for this unusual class of compounds was identified using metabologenomics and computational structure prediction data. Heterologous expression confirmed the BGC and suggests an unusual mechanism for trimethylammonium formation. Overall, the discovery of the tyrobetaines shows the great potential of metabologenomics combined with molecular networking and computational structure prediction for identifying interesting biosynthetic reactions and novel NPs.
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Affiliation(s)
- Elizabeth I. Parkinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James H. Tryon
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Anthony W. Goering
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kou-San Ju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ryan A. McClure
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeremy D. Kemball
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sara Zhukovsky
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - David P. Labeda
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - William W. Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801 United States
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31
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Song C, Zhu C, Wu Q, Qi J, Gao Y, Zhang Z, Gaur U, Yang D, Fan X, Yang M. Metabolome analysis of effect of aspirin on Drosophila lifespan extension. Exp Gerontol 2017; 95:54-62. [DOI: 10.1016/j.exger.2017.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/28/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
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32
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Gowda GAN, Raftery D. Whole Blood Metabolomics by 1H NMR Spectroscopy Provides a New Opportunity To Evaluate Coenzymes and Antioxidants. Anal Chem 2017; 89:4620-4627. [PMID: 28318242 PMCID: PMC6245939 DOI: 10.1021/acs.analchem.7b00171] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Conventional human blood metabolomics employs serum or plasma and provides a wealth of metabolic information therein. However, this approach lacks the ability to measure and evaluate important metabolites such as coenzymes and antioxidants that are present at high concentrations in red blood cells. As an important alternative to serum/plasma metabolomics, we show here that a simple 1H NMR experiment can simultaneously measure coenzymes and antioxidants in extracts of whole human blood, in addition to the nearly 70 metabolites that were shown to be quantitated in serum/plasma recently [ Anal. Chem. 2015 , 87 , 706 - 715 ]. Coenzymes of redox reactions: oxidized/reduced nicotinamide adenine dinucleotide (NAD+ and NADH) and nicotinamide adenine dinucleotide phosphate (NADP+ and NADPH); coenzymes of energy including adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP); and antioxidants, the sum of oxidized and reduced glutathione (GSSG and GSH) can be measured with essentially no additional effort. A new method was developed for detecting many of these unstable species without affecting other blood/blood plasma metabolites. The identities of coenzymes and antioxidants in blood NMR spectra were established combining 1D/2D NMR techniques, chemical shift databases, pH measurements and, finally, spiking with authentic compounds. This is the first study to report identification of major coenzymes and antioxidants and quantify them, simultaneously, with the large pool of other metabolites in human blood using NMR spectroscopy. Considering that the levels of coenzymes and antioxidants represent a sensitive measure of cellular functions in health and numerous diseases, the NMR method presented here potentially opens a new chapter in the metabolomics of blood.
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98109, United States
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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33
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Metabolomic study on the antihypertensive effect of S-1-propenylcysteine in spontaneously hypertensive rats using liquid chromatography coupled with quadrupole-Orbitrap mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1046:147-155. [PMID: 28183044 DOI: 10.1016/j.jchromb.2017.01.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 12/19/2022]
Abstract
Aged garlic extract (AGE) has been shown to improve hypertension in both clinical trials and experimental animal models. However, the active ingredient of AGE remains unknown. In the present study, we investigated the antihypertensive effects of AGE and its major constituents including S-1-propenylcysteine (S1PC) and S-allylcysteine (SAC) using spontaneously hypertensive rats (SHR) and found that S1PC is an active substance to lower blood pressure in SHR. In addition, the metabolomics approach was used to investigate the potential mechanism of the antihypertensive action of S1PC in SHR. Treatment with AGE (2g/kg body weight) or S1PC (6.5mg/kg body weight; equivalent to AGE 2g/kg body weight) significantly decreased the systolic blood pressure (SBP) of SHR after the repeated administration for 10 weeks, whereas treatment with SAC (7.9mg/kg body weight; equivalent to AGE 2g/kg body weight) did not decrease the SBP. After the treatment for 10 weeks, the plasma samples obtained from Wistar Kyoto (WKY) rats and SHR were analyzed by means of ultra high performance liquid chromatography coupled with high-resolution quadrupole-Orbitrap mass spectrometry. Multivariate statistical analysis of LC-MS data showed a clear difference in the metabolite profiles between WKY rats and SHR. The results indicated that 30 endogenous metabolites significantly contributed to the difference and 7 of 30 metabolites were changed by the S1PC treatment. Furthermore, regression analysis showed correlation between SBP and the plasma levels of betaine, tryptophan and 3 LysoPCs. This metabolomics approach suggested that S1PC could exert its antihypertensive effect by affecting glycine, serine and threonine metabolism, tryptophan metabolism and glycerophospholipid metabolism.
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34
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Turck D, Bresson J, Burlingame B, Dean T, Fairweather‐Tait S, Heinonen M, Hirsch‐Ernst KI, Mangelsdorf I, McArdle HJ, Naska A, Neuhäuser‐Berthold M, Nowicka G, Pentieva K, Sanz Y, Siani A, Sjödin A, Stern M, Tomé D, Vinceti M, Willatts P, Engel K, Marchelli R, Pöting A, Poulsen M, Schlatter J, Ackerl R, van Loveren H. Safety of synthetic l‐ergothioneine (Ergoneine®) as a novel food pursuant to Regulation (EC) No 258/97. EFSA J 2016. [DOI: 10.2903/j.efsa.2016.4629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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35
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Big data mining powers fungal research: recent advances in fission yeast systems biology approaches. Curr Genet 2016; 63:427-433. [PMID: 27730285 DOI: 10.1007/s00294-016-0657-4] [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: 09/23/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/05/2023]
Abstract
Biology research has entered into big data era. Systems biology approaches therefore become the powerful tools to obtain the whole landscape of how cell separate, grow, and resist the stresses. Fission yeast Schizosaccharomyces pombe is wonderful unicellular eukaryote model, especially studying its division and metabolism can facilitate to understanding the molecular mechanism of cancer and discovering anticancer agents. In this perspective, we discuss the recent advanced fission yeast systems biology tools, mainly focus on metabolomics profiling and metabolic modeling, protein-protein interactome and genetic interaction network, DNA sequencing and applications, and high-throughput phenotypic screening. We therefore hope this review can be useful for interested fungal researchers as well as bioformaticians.
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Reply to Mäkinen and Ala-Korpela: Small-scale but accurate metabolomics with high reproducibility for identifying age-related blood metabolites. Proc Natl Acad Sci U S A 2016; 113:E3471-2. [PMID: 27303026 DOI: 10.1073/pnas.1607149113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Individual variability in human blood metabolites identifies age-related differences. Proc Natl Acad Sci U S A 2016; 113:4252-9. [PMID: 27036001 DOI: 10.1073/pnas.1603023113] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Metabolites present in human blood document individual physiological states influenced by genetic, epigenetic, and lifestyle factors. Using high-resolution liquid chromatography-mass spectrometry (LC-MS), we performed nontargeted, quantitative metabolomics analysis in blood of 15 young (29 ± 4 y of age) and 15 elderly (81 ± 7 y of age) individuals. Coefficients of variation (CV = SD/mean) were obtained for 126 blood metabolites of all 30 donors. Fifty-five RBC-enriched metabolites, for which metabolomics studies have been scarce, are highlighted here. We found 14 blood compounds that show remarkable age-related increases or decreases; they include 1,5-anhydroglucitol, dimethyl-guanosine, acetyl-carnosine, carnosine, ophthalmic acid, UDP-acetyl-glucosamine,N-acetyl-arginine,N6-acetyl-lysine, pantothenate, citrulline, leucine, isoleucine, NAD(+), and NADP(+) Six of them are RBC-enriched, suggesting that RBC metabolomics is highly valuable for human aging research. Age differences are partly explained by a decrease in antioxidant production or increasing inefficiency of urea metabolism among the elderly. Pearson's coefficients demonstrated that some age-related compounds are correlated, suggesting that aging affects them concomitantly. Although our CV values are mostly consistent with those CVs previously published, we here report previously unidentified CVs of 51 blood compounds. Compounds having moderate to high CV values (0.4-2.5) are often modified. Compounds having low CV values, such as ATP and glutathione, may be related to various diseases because their concentrations are strictly controlled, and changes in them would compromise health. Thus, human blood is a rich source of information about individual metabolic differences.
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Abstract
Next-generation sequencing approaches have considerably advanced our understanding of genome function and regulation. However, the knowledge of gene function and complex cellular processes remains a challenge and bottleneck in biological research. Phenomics is a rapidly emerging area, which seeks to rigorously characterize all phenotypes associated with genes or gene variants. Such high-throughput phenotyping under different conditions can be a potent approach toward gene function. The fission yeast Schizosaccharomyces pombe (S. pombe) is a proven eukaryotic model organism that is increasingly used for genomewide screens and phenomic assays. In this review, we highlight current large-scale, cell-based approaches used with S. pombe, including computational colony-growth measurements, genetic interaction screens, parallel profiling using barcodes, microscopy-based cell profiling, metabolomic methods and transposon mutagenesis. These diverse methods are starting to offer rich insights into the relationship between genotypes and phenotypes.
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Affiliation(s)
- Charalampos Rallis
- a Research Department of Genetics , Evolution and Environment and UCL Institute of Healthy Ageing, University College London , London , UK
| | - Jürg Bähler
- a Research Department of Genetics , Evolution and Environment and UCL Institute of Healthy Ageing, University College London , London , UK
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Stanstrup J, Neumann S, Vrhovšek U. PredRet: prediction of retention time by direct mapping between multiple chromatographic systems. Anal Chem 2015; 87:9421-8. [PMID: 26289378 DOI: 10.1021/acs.analchem.5b02287] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Demands in research investigating small molecules by applying untargeted approaches have been a key motivator for the development of repositories for mass spectrometry spectra and automated tools to aid compound identification. Comparatively little attention has been afforded to using retention times (RTs) to distinguish compounds and for liquid chromatography there are currently no coordinated efforts to share and exploit RT information. We therefore present PredRet; the first tool that makes community sharing of RT information possible across laboratories and chromatographic systems (CSs). At http://predret.org , a database of RTs from different CSs is available and users can upload their own experimental RTs and download predicted RTs for compounds which they have not experimentally determined in their own experiments. For each possible pair of CSs in the database, the RTs are used to construct a projection model between the RTs in the two CSs. The number of compounds for which RTs can be predicted and the accuracy of the predictions are dependent upon the compound coverage overlap between the CSs used for construction of projection models. At the moment, it is possible to predict up to 400 RTs with a median error between 0.01 and 0.28 min depending on the CS and the median width of the prediction interval ranging from 0.08 to 1.86 min. By comparing experimental and predicted RTs, the user can thus prioritize which isomers to target for further characterization and potentially exclude some structures completely. As the database grows, the number and accuracy of predictions will increase.
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Affiliation(s)
- Jan Stanstrup
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM) , Via E. Mach 1, 38010 San Michele all'Adige, Trentiono, Italy
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle, Germany
| | - Urška Vrhovšek
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM) , Via E. Mach 1, 38010 San Michele all'Adige, Trentiono, Italy
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D'Alessandro A, Slaughter AL, Peltz ED, Moore EE, Silliman CC, Wither M, Nemkov T, Bacon AW, Fragoso M, Banerjee A, Hansen KC. Trauma/hemorrhagic shock instigates aberrant metabolic flux through glycolytic pathways, as revealed by preliminary (13)C-glucose labeling metabolomics. J Transl Med 2015; 13:253. [PMID: 26242576 PMCID: PMC4523956 DOI: 10.1186/s12967-015-0612-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/20/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Metabolic derangement is a key hallmark of major traumatic injury. The recent introduction of mass spectrometry-based metabolomics technologies in the field of trauma shed new light on metabolic aberrations in plasma that are triggered by trauma and hemorrhagic shock. Alteration in metabolites associated with catabolism, acidosis and hyperglycemia have been identified. However, the mechanisms underlying fluxes driving such metabolic adaptations remain elusive. METHODS A bolus of U-(13)C-glucose was injected in Sprague-Dawley rats at different time points. Plasma extracts were analyzed via ultra-high performance liquid chromatography-mass spectrometry to detect quantitative fluctuations in metabolite levels as well as to trace the distribution of heavy labeled carbon isotopologues. RESULTS Rats experiencing trauma did not show major plasma metabolic aberrations. However, trauma/hemorrhagic shock triggered severe metabolic derangement, resulting in increased glucose levels, lactate and carboxylic acid accumulation. Isotopologue distributions in late Krebs cycle metabolites (especially succinate) suggested a blockade at complex I and II of the electron transport chain, likely due to mitochondrial uncoupling. Urate increased after trauma and hemorrhage. Increased levels of unlabeled mannitol and citramalate, metabolites of potential bacterial origin, were also observed in trauma/hemorrhagic shock rats, but not trauma alone or controls. CONCLUSIONS These preliminary results are consistent with observations we have recently obtained in humans, and expand upon our early results on rodent models of trauma and hemorrhagic shock by providing the kinetics of glucose fluxes after trauma and hemorrhage. Despite the preliminary nature of this study, owing to the limited number of biological replicates, results highlight a role for shock, rather than trauma alone, in eliciting systemic metabolic aberrations. This study provides the foundation for tracing experiments in rat models of trauma. The goal is to improve our understanding of substrate specific metabolic derangements in trauma/hemorrhagic shock, so as to design resuscitative strategies tailored toward metabolic alterations and the severity of trauma.
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Affiliation(s)
- Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, East 17th Ave, Aurora, CO, 12801, USA.
| | | | - Erik D Peltz
- Department of Surgery, University of Colorado, Aurora, CO, USA.
| | - Ernest E Moore
- Department of Surgery, University of Colorado, Aurora, CO, USA.
- Denver Health Medical Center, Denver, CO, USA.
| | - Christopher C Silliman
- Department of Surgery, University of Colorado, Aurora, CO, USA.
- Bonfils Blood Center, Denver, CO, USA.
| | - Matthew Wither
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, East 17th Ave, Aurora, CO, 12801, USA.
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, East 17th Ave, Aurora, CO, 12801, USA.
| | - Anthony W Bacon
- Department of Surgery, University of Colorado, Aurora, CO, USA.
| | - Miguel Fragoso
- Department of Surgery, University of Colorado, Aurora, CO, USA.
- Denver Health Medical Center, Denver, CO, USA.
| | | | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, East 17th Ave, Aurora, CO, 12801, USA.
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Lawson AJ, Bernstone L, Hall SK. Newborn screening blood spot analysis in the UK: influence of spot size, punch location and haematocrit. J Med Screen 2015; 23:7-16. [DOI: 10.1177/0969141315593571] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/20/2015] [Indexed: 11/16/2022]
Abstract
Objective In dried blood spot analysis, punch location and variations in applied sample volume and haematocrit can produce different measured concentrations of analytes. We investigated the magnitude of these effects in newborn screening in the UK. Methods Heparinized blood spiked with thyroid stimulating hormone (TSH), phenylalanine, tyrosine, leucine, methionine, octanoyl carnitine (C8), and immunoreactive trypsinogen (IRT) was spotted onto filter paper: (i) at a constant haematocrit of 50% at various volumes, and (ii) at a range of haematocrits using a constant volume. Subpunches (3.2 mm) of the dried blood spots were then analysed. Results Compared with a central punch from a 50 µL blood spot with 50% haematocrit, 10 µL spots can have significantly lower measured concentrations of all analytes, with decreases of 15% or more observed for leucine, methionine, phenylalanine, and tyrosine. Punching at the edge of a spot can increase measured concentrations up to 35%. Higher haematocrit decreased measured TSH and C8 yet increased amino acids and IRT by 15% compared with 50% haematocrit. Lower haematocrits had the opposite effect, but only with higher concentrations of some analytes. Conclusions Differences in blood spot size, haematocrit and punch location substantially affect measured concentrations for analytes used in the UK newborn screening programme, and this could affect false positive and negative rates. To minimize analytical bias, these variables should be controlled or adjusted for where possible.
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Affiliation(s)
- AJ Lawson
- Department of Newborn Screening and Biochemical Genetics, Birmingham Children's Hospital, Birmingham, B4 6NH
- Department of Biochemistry and Immunology, Birmingham Heartlands Hospital, Birmingham, B9 5ST
| | - L Bernstone
- Department of Newborn Screening and Biochemical Genetics, Birmingham Children's Hospital, Birmingham, B4 6NH
- Department of Clinical Biochemistry, Wythenshawe Hospital, University Hospital of South Manchester NHS Foundation Trust, Manchester, M23 9LT
| | - SK Hall
- Department of Newborn Screening and Biochemical Genetics, Birmingham Children's Hospital, Birmingham, B4 6NH
- UK Newborn Screening Laboratories Network
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Pathologic metabolism: an exploratory study of the plasma metabolome of critical injury. J Trauma Acute Care Surg 2015; 78:742-51. [PMID: 25807403 DOI: 10.1097/ta.0000000000000589] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Severe trauma is associated with massive alterations in metabolism. Thus far, investigations have relied on traditional bioanalytic approaches including calorimetry or nuclear magnetic resonance. However, recent strides in mass spectrometry (MS)-based metabolomics present enhanced analytic opportunities to characterize a wide range of metabolites in the critical care setting. METHODS MS-based metabolomics analyses were performed on plasma samples from severely injured patients' trauma activation field blood and plasma samples obtained during emergency department thoracotomy. These were compared against the metabolic profiles of healthy controls. RESULTS Few significant alterations were observed between trauma activation field blood and emergency department thoracotomy patients. In contrast, we identified trauma-dependent metabolic signatures, which support a state of hypercatabolism, driven by sugar consumption, lipolysis and fatty acid use, accumulation of ketone bodies, proteolysis and nucleoside breakdown, which provides carbon and nitrogen sources to compensate for trauma-induced energy consumption and negative nitrogen balance. Unexpectedly, metabolites of bacterial origin (including tricarballylate and citramalate) were detected in plasma from trauma patients. CONCLUSION In the future, the correlation between metabolomics adaptation and recovery outcomes could be studied by MS-based approaches, and this work can provide a method for assessing the efficacy of alternative resuscitation strategies.
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D'Alessandro A, Moore HB, Moore EE, Wither M, Nemkov T, Gonzalez E, Slaughter A, Fragoso M, Hansen KC, Silliman CC, Banerjee A. Early hemorrhage triggers metabolic responses that build up during prolonged shock. Am J Physiol Regul Integr Comp Physiol 2015; 308:R1034-44. [PMID: 25876652 DOI: 10.1152/ajpregu.00030.2015] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/13/2015] [Indexed: 12/13/2022]
Abstract
Metabolic staging after trauma/hemorrhagic shock is a key driver of acidosis and directly relates to hypothermia and coagulopathy. Metabolic responses to trauma/hemorrhagic shock have been assayed through classic biochemical approaches or NMR, thereby lacking a comprehensive overview of the dynamic metabolic changes occurring after shock. Sprague-Dawley rats underwent progressive hemorrhage and shock. Baseline and postshock blood was collected, and late hyperfibrinolysis was assessed (LY30 >3%) in all of the tested rats. Extreme and intermediate time points were collected to assay the dynamic changes of the plasma metabolome via ultra-high performance liquid chromatography-mass spectrometry. Sham controls were used to determine whether metabolic changes could be primarily attributable to anesthesia and supine positioning. Early hemorrhage-triggered metabolic changes that built up progressively and became significant during sustained hemorrhagic shock. Metabolic phenotypes either resulted in immediate hypercatabolism, or late hypercatabolism, preceded by metabolic deregulation during early hemorrhage in a subset of rats. Hemorrhagic shock consistently promoted hyperglycemia, glycolysis, Krebs cycle, fatty acid, amino acid, and nitrogen metabolism (urate and polyamines), and impaired redox homeostasis. Early dynamic changes of the plasma metabolome are triggered by hemorrhage in rats. Future studies will determine whether metabolic subphenotypes observed in rats might be consistently observed in humans and pave the way for tailored resuscitative strategies.
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Affiliation(s)
- Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, South, Aurora, Colorado;
| | - Hunter B Moore
- Department of Surgery/Trauma Research Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Ernest E Moore
- Department of Surgery/Trauma Research Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado; Department of Surgery, Denver Health Medical Center, Denver, Colorado
| | - Matthew Wither
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, South, Aurora, Colorado
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, South, Aurora, Colorado
| | - Eduardo Gonzalez
- Department of Surgery/Trauma Research Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Anne Slaughter
- Department of Surgery/Trauma Research Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Miguel Fragoso
- Department of Surgery/Trauma Research Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, South, Aurora, Colorado
| | - Christopher C Silliman
- Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, Colorado; and Research Laboratory, Bonfils Blood Center, Denver, Colorado
| | - Anirban Banerjee
- Department of Surgery/Trauma Research Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
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Murakami I, Chaleckis R, Pluskal T, Ito K, Hori K, Ebe M, Yanagida M, Kondoh H. Metabolism of skin-absorbed resveratrol into its glucuronized form in mouse skin. PLoS One 2014; 9:e115359. [PMID: 25506824 PMCID: PMC4266648 DOI: 10.1371/journal.pone.0115359] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 11/22/2014] [Indexed: 01/24/2023] Open
Abstract
Resveratrol (RESV) is a plant polyphenol, which is thought to have beneficial metabolic effects in laboratory animals as well as in humans. Following oral administration, RESV is immediately catabolized, resulting in low bioavailability. This study compared RESV metabolites and their tissue distribution after oral uptake and skin absorption. Metabolomic analysis of various mouse tissues revealed that RESV can be absorbed and metabolized through skin. We detected sulfated and glucuronidated RESV metabolites, as well as dihydroresveratrol. These metabolites are thought to have lower pharmacological activity than RESV. Similar quantities of most RESV metabolites were observed 4 h after oral or skin administration, except that glucuronidated RESV metabolites were more abundant in skin after topical RESV application than after oral administration. This result is consistent with our finding of glucuronidated RESV metabolites in cultured skin cells. RESV applied to mouse ears significantly suppressed inflammation in the TPA inflammation model. The skin absorption route could be a complementary, potent way to achieve therapeutic effects with RESV.
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Affiliation(s)
- Itsuo Murakami
- Geriatric unit, Kyoto University Hospital, Sakyo-ku, Kyoto, Japan
| | - Romanas Chaleckis
- Geriatric unit, Kyoto University Hospital, Sakyo-ku, Kyoto, Japan
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Tomáš Pluskal
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Ken Ito
- Geriatric unit, Kyoto University Hospital, Sakyo-ku, Kyoto, Japan
| | - Kousuke Hori
- Geriatric unit, Kyoto University Hospital, Sakyo-ku, Kyoto, Japan
| | - Masahiro Ebe
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
- * E-mail: (HK); (MY)
| | - Hiroshi Kondoh
- Geriatric unit, Kyoto University Hospital, Sakyo-ku, Kyoto, Japan
- * E-mail: (HK); (MY)
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