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Uzan-Yulzari A, Turjeman S, Moadi L, Getselter D, Sharon E, Rautava S, Isolauri E, Khatib S, Elliott E, Koren O. A gut reaction? The role of the microbiome in aggression. Brain Behav Immun 2024; 122:301-312. [PMID: 39128572 DOI: 10.1016/j.bbi.2024.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/14/2024] [Accepted: 08/08/2024] [Indexed: 08/13/2024] Open
Abstract
Recent research has unveiled conflicting evidence regarding the link between aggression and the gut microbiome. Here, we compared behavior profiles of control, germ-free (GF), and antibiotic-treated mice, as well as re-colonized GF mice to understand the impact of the gut microbiome on aggression using the resident-intruder paradigm. Our findings revealed a link between gut microbiome depletion and higher aggression, accompanied by notable changes in urine metabolite profiles and brain gene expression. This study extends beyond classical murine models to humanized mice to reveal the clinical relevance of early-life antibiotic use on aggression. Fecal microbiome transplant from infants exposed to antibiotics in early life (and sampled one month later) into mice led to increased aggression compared to mice receiving transplants from unexposed infants. This study sheds light on the role of the gut microbiome in modulating aggression and highlights its potential avenues of action, offering insights for development of therapeutic strategies for aggression-related disorders.
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Affiliation(s)
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Lelyan Moadi
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Efrat Sharon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Samuli Rautava
- Department of Clinical Sciences, Faculty of Medicine, University of Turku, Turku, Finland; Department of Pediatrics, University of Helsinki and New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Erika Isolauri
- Department of Clinical Sciences, Faculty of Medicine, University of Turku, Turku, Finland; Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Soliman Khatib
- Department of Natural Compounds and Analytical Chemistry, Migal-Galilee Research Institute, Kiryat Shmona, Israel; Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel
| | - Evan Elliott
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel; Kyung Hee University, Seoul, Republic of Korea.
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2
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Chen B, Li H, Huang R, Tang Y, Li F. Deep learning prediction of electrospray ionization tandem mass spectra of chemically derived molecules. Nat Commun 2024; 15:8396. [PMID: 39333165 PMCID: PMC11436754 DOI: 10.1038/s41467-024-52805-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 09/16/2024] [Indexed: 09/29/2024] Open
Abstract
Chemical derivatization is a powerful strategy to enhance sensitivity and selectivity of liquid chromatography-mass spectrometry for non-targeted analysis of chemicals in complex mixtures. However, it remains impossible to obtain large sets of reference spectra for chemically derived molecules (CDMs), representing a major barrier in real-world applications. Herein, we describe a deep learning approach that enables accurate prediction of electrospray ionization tandem mass spectra for CDMs (DeepCDM). DeepCDM is established by transfer learning from a generic spectrum predicting model using a small set of experimentally acquired tandem mass spectra of CDMs, which converts a generic model with low predictability for CDMs into a specialized model with high predictability. We demonstrate DeepCDM by predicting electrospray ionization tandem mass spectra of dansylated molecules. The success in establishing Dns-MS further enables the development of DnsBank, a dansylation-specialized in silico spectral library. DnsBank achieves significant increases of accurate annotation rates of dansylated molecules, facilitating discovery of new hazardous pollutants from an environmental study of leather industrial wastewater. DeepCDM is also highly versatile for other classes of CDMs. Therefore, we envision that DeepCDM will pave a way for high-throughput identification of CDMs in non-targeted analysis to dig unknowns with potential health impacts from emerging anthropogenic chemicals.
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Affiliation(s)
- Bin Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Hailiang Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Rongfu Huang
- Sichuan Provincial Key Laboratory of Universities on Environmental Science and Engineering, MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Yanan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, 610064, China.
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, China.
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3
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González-Domínguez Á, Savolainen O, Domínguez-Riscart J, Landberg R, Lechuga-Sancho A, González-Domínguez R. Probing erythrocytes as sensitive and reliable sensors of metabolic disturbances in the crosstalk between childhood obesity and insulin resistance: findings from an observational study, in vivo challenge tests, and ex vivo incubation assays. Cardiovasc Diabetol 2024; 23:336. [PMID: 39261864 PMCID: PMC11391635 DOI: 10.1186/s12933-024-02395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 08/07/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Although insulin resistance (IR) is among the most frequent and pathogenically relevant complications accompanying childhood obesity, its role in modulating and exacerbating obesity pathophysiology has not yet been completely clarified. METHODS To get deeper insights into the interplay between childhood obesity and IR, we leveraged a comprehensive experimental design based on a combination of observational data, in vivo challenge tests (i.e., oral glucose tolerance test), and ex vivo assays (i.e., incubation of erythrocytes with insulin) using a population comprising children with obesity and IR, children with obesity without IR, and healthy controls, from whom plasma and erythrocyte samples were collected for subsequent metabolomics analysis. RESULTS Children with concomitant IR showed exacerbated metabolic disturbances in the crosstalk between endogenous, microbial, and environmental determinants, including failures in energy homeostasis, amino acid metabolism, oxidative stress, synthesis of steroid hormones and bile acids, membrane lipid composition, as well as differences in exposome-related metabolites associated with diet, exposure to endocrine disruptors, and gut microbiota. Furthermore, challenge tests and ex vivo assays revealed a deleterious impact of IR on individuals' metabolic flexibility, as reflected in blunted capacity to regulate homeostasis in response to hyperinsulinemia, at both systemic and erythroid levels. CONCLUSIONS Thus, we have demonstrated for the first time that metabolite alterations in erythrocytes represent reliable and sensitive biomarkers to disentangle the metabolic complexity of IR and childhood obesity. This study emphasizes the crucial need of addressing inter-individual variability factors, such as the presence of comorbidities, to obtain a more accurate understanding of obesity-related molecular mechanisms.
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Affiliation(s)
- Álvaro González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Otto Savolainen
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Jesús Domínguez-Riscart
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
- Unidad de Endocrinología Pediátrica y Diabetes, Servicio de Pediatría, Hospital Universitario Puerta del Mar, Cádiz, 11009, Spain
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Alfonso Lechuga-Sancho
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
- Unidad de Endocrinología Pediátrica y Diabetes, Servicio de Pediatría, Hospital Universitario Puerta del Mar, Cádiz, 11009, Spain
- Departamento Materno Infantil y Radiología, Facultad de Medicina, Universidad de Cádiz, Cádiz, 11009, Spain
| | - Raúl González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain.
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Ribeiro da Silva Lima L, Barros Santos MC, P. Gomes PW, Fernández-Ochoa Á, Simões Larraz Ferreira M. Overview of the Metabolite Composition and Antioxidant Capacity of Seven Major and Minor Cereal Crops and Their Milling Fractions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19197-19218. [PMID: 38803291 PMCID: PMC11363145 DOI: 10.1021/acs.jafc.4c01312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Cereal grains play an important role in human health as a source of macro- and micronutrients, besides phytochemicals. The metabolite diversity was investigated in cereal crops and their milling fractions by untargeted metabolomics ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) of 69 samples: 7 species (barley, oat, pearl millet, rye, sorghum, triticale, and wheat), 23 genotypes, and 4 milling fractions (husk, bran, flour, and wholegrain). Samples were also analyzed by in vitro antioxidant activity. UHPLC-MS/MS signals were processed using XCMS, and metabolite annotation was based on SIRIUS and GNPS libraries. Bran and husk showed the highest antioxidant capacity and phenolic content/diversity. The major metabolite classes were phenolic acids, flavonoids, fatty acyls, and organic acids. Sorghum, millet, barley, and oats showed distinct metabolite profiles, especially related to the bran fraction. Molecular networking and chemometrics provided a comprehensive insight into the metabolic profiling of cereal crops, unveiling the potential of coproducts and super cereals such as sorghum and millet as sources of polyphenols.
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Affiliation(s)
- Luciana Ribeiro da Silva Lima
- Laboratory
of Bioactives, Food and Nutrition Graduate Program (PPGAN), Federal University of the State of Rio de Janeiro
(UNIRIO), Rio de Janeiro 22290-240, Brazil
- Center
of Innovation in Mass Spectrometry, Laboratory of Protein Biochemistry, UNIRIO, Rio de
Janeiro 22290-240, Brazil
| | - Millena C. Barros Santos
- Bordeaux
Metabolome-MetaboHUB, INRAE Bordeaux Nouvelle-Aquitaine,
UMR1332 BFP, Villenave
d’Ornon 33882, France
| | - Paulo Wender P. Gomes
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy &
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman
Drive, La Jolla, San Diego, California 92093-0751, United States
| | - Álvaro Fernández-Ochoa
- Department
of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Mariana Simões Larraz Ferreira
- Laboratory
of Bioactives, Food and Nutrition Graduate Program (PPGAN), Federal University of the State of Rio de Janeiro
(UNIRIO), Rio de Janeiro 22290-240, Brazil
- Center
of Innovation in Mass Spectrometry, Laboratory of Protein Biochemistry, UNIRIO, Rio de
Janeiro 22290-240, Brazil
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5
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González-Domínguez Á, Domínguez-Riscart J, Savolainen O, Lechuga-Sancho A, Landberg R, González-Domínguez R. Identifying metabotypes of insulin resistance severity in children with metabolic syndrome. Cardiovasc Diabetol 2024; 23:315. [PMID: 39192263 DOI: 10.1186/s12933-024-02412-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Insulin resistance is a frequent precursor of typical obesity and metabolic syndrome complications. However, accurate diagnosis remains elusive because of its pathophysiological complexity and heterogeneity. Herein, we have explored the utility of insulin secretion dynamics in response to an oral glucose tolerance test as a surrogate marker to identify distinct metabotypes of disease severity. METHODS The study population consisted of children with obesity and insulin resistance, stratified according to the post-challenge insulin peak timing (i.e., early, middle, and late peak), from whom fasting and postprandial plasma and erythrocytes were collected for metabolomics analysis. RESULTS Children with late insulin peak manifested worse cardiometabolic health (i.e., higher blood pressure, glycemia, and HOMA-IR scores) than early responders. These subjects also showed more pronounced changes in metabolites mirroring failures in energy homeostasis, oxidative stress, metabolism of cholesterol and phospholipids, and adherence to unhealthy dietary habits. Furthermore, delayed insulin peak was associated with impaired metabolic flexibility, as reflected in compromised capacity to regulate mitochondrial energy pathways and the antioxidant defense in response to glucose overload. CONCLUSIONS Altogether, these findings suggest that insulin resistance could encompass several phenotypic subtypes characterized by graded disturbances in distinctive metabolic derangements occurring in childhood obesity, which serve as severity predictive markers.
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Affiliation(s)
- Álvaro González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Jesús Domínguez-Riscart
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
- Unidad de Endocrinología Pediátrica y Diabetes, Servicio de Pediatría, Hospital Universitario Puerta del Mar, Cádiz, 11009, Spain
| | - Otto Savolainen
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Alfonso Lechuga-Sancho
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain
- Unidad de Endocrinología Pediátrica y Diabetes, Servicio de Pediatría, Hospital Universitario Puerta del Mar, Cádiz, 11009, Spain
- Departamento Materno Infantil y Radiología, Facultad de Medicina, Universidad de Cádiz, Cádiz, 11009, Spain
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Raúl González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, 11009, Spain.
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6
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Essex M, Millet Pascual-Leone B, Löber U, Kuhring M, Zhang B, Brüning U, Fritsche-Guenther R, Krzanowski M, Fiocca Vernengo F, Brumhard S, Röwekamp I, Anna Bielecka A, Lesker TR, Wyler E, Landthaler M, Mantei A, Meisel C, Caesar S, Thibeault C, Corman VM, Marko L, Suttorp N, Strowig T, Kurth F, Sander LE, Li Y, Kirwan JA, Forslund SK, Opitz B. Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19. NPJ Biofilms Microbiomes 2024; 10:66. [PMID: 39085233 PMCID: PMC11291933 DOI: 10.1038/s41522-024-00538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.
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Affiliation(s)
- Morgan Essex
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Belén Millet Pascual-Leone
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mathias Kuhring
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Core Unit Bioinformatics, Berlin, Germany
| | - Bowen Zhang
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, joint ventures between the Helmholtz Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ulrike Brüning
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
| | | | - Marta Krzanowski
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Facundo Fiocca Vernengo
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sophia Brumhard
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ivo Röwekamp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Agata Anna Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Christian Meisel
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra Caesar
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Victor M Corman
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Lajos Marko
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Till Strowig
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Florian Kurth
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Yang Li
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, joint ventures between the Helmholtz Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Jennifer A Kirwan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
- University of Nottingham School of Veterinary Medicine and Science, Loughborough, UK
| | - Sofia K Forslund
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bastian Opitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany.
- German Center for Lung Research (DZL), Berlin, Germany.
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7
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Ollennu-Chuasam P, Ahmed H, Koistinen V, Hanhineva K, Linderborg KM, Suomela JP. Lipophilic and Hydrophilic Metabolites as Descriptors of Different Coffee Beverages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16461-16474. [PMID: 38984670 DOI: 10.1021/acs.jafc.4c03347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Coffee is a widely consumed beverage rich in bioactive phytochemicals. This study investigated the effect of brewing method on the profile of potential bioactive compounds in different coffee beverages using metabolomics and lipidomics based on UHPLC-MS/QTOF. The oil contents of the espresso coffee (EC), pot coffee (PC), instant coffee (IC), and filter coffee (FC) beverages studied were 0.13% ± 0.002, 0.12% ± 0.001, 0.04% ± 0.002, and 0.03% ± 0.003, respectively. Univariate analysis indicated significant differences (P < 0.001) in oil content when EC and PC beverages were compared with IC and FC beverages. Principal component analysis revealed similarities in the lipid profiles of FC and EC beverages and the hydrophilic profiles of PC and FC beverages. The EC beverage had the highest intensity of hydrophilic compounds such as adenine, theobromine, chlorogenic acid, and caffeine. The PC beverage was the most abundant in triglycerides, phosphatidylcholine, and diterpenes. Cafestol and kahweol esters, but not their free forms, were the most abundant diterpenes in the PC beverage. This work provides information on the differences in the profile of potentially bioactive compounds in four commonly consumed coffee beverage types and, thus, on the possible differences in the health effects of these coffee beverage types.
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Affiliation(s)
| | - Hany Ahmed
- Food Sciences, Department of Life Technologies, University of Turku, Turku 20014, Finland
| | - Ville Koistinen
- Food Sciences, Department of Life Technologies, University of Turku, Turku 20014, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio 70211, Finland
| | - Kati Hanhineva
- Food Sciences, Department of Life Technologies, University of Turku, Turku 20014, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio 70211, Finland
| | - Kaisa M Linderborg
- Food Sciences, Department of Life Technologies, University of Turku, Turku 20014, Finland
| | - Jukka-Pekka Suomela
- Food Sciences, Department of Life Technologies, University of Turku, Turku 20014, Finland
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8
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Healy DR, Zarei I, Mikkonen S, Soininen S, Viitasalo A, Haapala EA, Auriola S, Hanhineva K, Kolehmainen M, Lakka TA. Longitudinal associations of an exposome score with serum metabolites from childhood to adolescence. Commun Biol 2024; 7:890. [PMID: 39039257 PMCID: PMC11263428 DOI: 10.1038/s42003-024-06146-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 04/05/2024] [Indexed: 07/24/2024] Open
Abstract
Environmental and lifestyle factors, including air pollution, impaired diet, and low physical activity, have been associated with cardiometabolic risk factors in childhood and adolescence. However, environmental and lifestyle exposures do not exert their physiological effects in isolation. This study investigated associations between an exposome score to measure the impact of multiple exposures, including diet, physical activity, sleep duration, air pollution, and socioeconomic status, and serum metabolites measured using LC-MS and NMR, compared to the individual components of the score. A general population of 504 children aged 6-9 years at baseline was followed up for eight years. Data were analysed with linear mixed-effects models using the R software. The exposome score was associated with 31 metabolites, of which 12 metabolites were not associated with any individual exposure category. These findings highlight the value of a composite score to predict metabolic changes associated with multiple environmental and lifestyle exposures since childhood.
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Affiliation(s)
- Darren R Healy
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio Campus, Finland.
| | - Iman Zarei
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio Campus, Finland
| | - Santtu Mikkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Finland
- Department of Technical Physics, University of Eastern Finland, Kuopio Campus, Finland
| | - Sonja Soininen
- Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, Finland
- Physician and Nursing Services, Health and Social Services Centre, Wellbeing Services County of North Savo, Varkaus, Finland
| | - Anna Viitasalo
- Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Eero A Haapala
- Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio Campus, Finland
- LC-MS Metabolomics Center, Biocenter Kuopio, Kuopio, Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio Campus, Finland
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
| | - Marjukka Kolehmainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio Campus, Finland
| | - Timo A Lakka
- Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
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9
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Moadi L, Turjeman S, Asulin N, Koren O. The effect of testosterone on the gut microbiome in mice. Commun Biol 2024; 7:880. [PMID: 39030253 PMCID: PMC11271554 DOI: 10.1038/s42003-024-06470-5] [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: 10/19/2023] [Accepted: 06/19/2024] [Indexed: 07/21/2024] Open
Abstract
The role of hormones in gut-brain crosstalk is largely elusive, but recent research supports specific changes in hormone levels correlated with the gut microbiota. An interesting but unstudied area in microbial endocrinology is the interplay between the microbiota and sex hormones. The aim of this study is to investigate the effect of testosterone and sex on the mouse gut microbiome. We use in vitro experiments to test direct effects of testosterone on bacteria in fecal samples collected from male and female mice pre- and post-puberty. Sex-specific microbial and metabolic differences surrounding puberty are also examined in vivo. We then explore effects of testosterone supplementation in vivo, characterizing microbiota and metabolomes of male and female mice. We detect sex-specific differences in microbiota and associated metabolites of mice post-puberty, but in vitro experiments reveal that testosterone only affects microbiota of fecal samples collected before puberty. Testosterone supplementation in vivo affects gut microbiota and metabolomes in both male and female mice. Taking our results from in vitro and in vivo experiments, we conclude that the shift in the microbiome after puberty is at least partially caused by the higher levels of sex hormones, mainly testosterone, in the host.
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Affiliation(s)
- Lelyan Moadi
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Nofar Asulin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
- Kyung Hee University, Seoul, Republic of Korea.
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10
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Zarei I, Eloranta AM, Klåvus A, Väistö J, Lehtonen M, Mikkonen S, Koistinen VM, Sallinen T, Haapala EA, Lintu N, Soininen S, Haikonen R, Atalay M, Schwab U, Auriola S, Kolehmainen M, Hanhineva K, Lakka TA. Eight-year diet and physical activity intervention affects serum metabolites during childhood and adolescence: A nonrandomized controlled trial. iScience 2024; 27:110295. [PMID: 39055945 PMCID: PMC11269805 DOI: 10.1016/j.isci.2024.110295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/16/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Long-term lifestyle interventions in childhood and adolescence can significantly improve cardiometabolic health, but the underlying molecular mechanisms remain poorly understood. To address this knowledge gap, we conducted an 8-year diet and physical activity intervention in a general population of children. The research revealed that the intervention influenced 80 serum metabolites over two years, with 17 metabolites continuing to be affected after eight years. The intervention primarily impacted fatty amides, including palmitic amide, linoleamide, oleamide, and others, as well as unsaturated fatty acids, acylcarnitines, phospholipids, sterols, gut microbiota-derived metabolites, amino acids, and purine metabolites. Particularly noteworthy were the pronounced changes in serum fatty amides. These serum metabolite alterations could represent molecular mechanisms responsible for the observed benefits of long-term lifestyle interventions on cardiometabolic and overall health since childhood. Understanding these metabolic changes may provide valuable insights into the prevention of cardiometabolic and other non-communicable diseases since childhood.
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Affiliation(s)
- Iman Zarei
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Aino-Maija Eloranta
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Juuso Väistö
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, Kuopio, Finland
- LC-MS Metabolomics Center, Biocenter Kuopio, Kuopio, Finland
| | - Santtu Mikkonen
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ville M. Koistinen
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Food Chemistry and Food Development Unit, Department of Biochemistry, University of Turku, Turku, Finland
| | - Taisa Sallinen
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Eero A. Haapala
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Niina Lintu
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Sonja Soininen
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Physician and Nursing Services, Health and Social Services Centre, Wellbeing Services County of North Savo, Varkaus, Finland
| | - Retu Haikonen
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ursula Schwab
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, Kuopio, Finland
| | - Marjukka Kolehmainen
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Food Chemistry and Food Development Unit, Department of Biochemistry, University of Turku, Turku, Finland
| | - Timo A. Lakka
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
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11
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Fernandez-Cantos MV, Babu AF, Hanhineva K, Kuipers OP. Identification of metabolites produced by six gut commensal Bacteroidales strains using non-targeted LC-MS/MS metabolite profiling. Microbiol Res 2024; 283:127700. [PMID: 38518452 DOI: 10.1016/j.micres.2024.127700] [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: 12/15/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024]
Abstract
As the most abundant gram-negative bacterial order in the gastrointestinal tract, Bacteroidales bacteria have been extensively studied for their contribution to various aspects of gut health. These bacteria are renowned for their involvement in immunomodulation and their remarkable capacity to break down complex carbohydrates and fibers. However, the human gut microbiota is known to produce many metabolites that ultimately mediate important microbe-host and microbe-microbe interactions. To gain further insights into the metabolites produced by the gut commensal strains of this order, we examined the metabolite composition of their bacterial cell cultures in the stationary phase. Based on their abundance in the gastrointestinal tract and their relevance in health and disease, we selected a total of six bacterial strains from the relevant genera Bacteroides, Phocaeicola, Parabacteroides, and Segatella. We grew these strains in modified Gifu anaerobic medium (mGAM) supplemented with mucin, which resembles the gut microbiota's natural environment. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolite profiling revealed 179 annotated metabolites that had significantly differential abundances between the studied bacterial strains and the control growth medium. Most of them belonged to classes such as amino acids and derivatives, organic acids, and nucleot(s)ides. Of particular interest, Segatella copri DSM 18205 (previously referred to as Prevotella copri) produced substantial quantities of the bioactive metabolites phenylethylamine, tyramine, tryptamine, and ornithine. Parabacteroides merdae CL03T12C32 stood out due to its ability to produce cadaverine, histamine, acetylputrescine, and deoxycarnitine. In addition, we found that strains of the genera Bacteroides, Phocaeicola, and Parabacteroides accumulated considerable amounts of proline-hydroxyproline, a collagen-derived bioactive dipeptide. Collectively, these findings offer a more detailed comprehension of the metabolic potential of these Bacteroidales strains, contributing to a better understanding of their role within the human gut microbiome in health and disease.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Ambrin Farizah Babu
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, Kuopio 70210, Finland
| | - Kati Hanhineva
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, Kuopio 70210, Finland; Department of Life Technologies, Food Sciences Unit, University of Turku, Turku 20014, Finland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
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12
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Babu AF, Palomurto S, Kärjä V, Käkelä P, Lehtonen M, Hanhineva K, Pihlajamäki J, Männistö V. Metabolic signatures of metabolic dysfunction-associated steatotic liver disease in severely obese patients. Dig Liver Dis 2024:S1590-8658(24)00773-4. [PMID: 38825414 DOI: 10.1016/j.dld.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/02/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024]
Abstract
BACKROUND Metabolic dysfunction-associated steatotic liver disease (MASLD) can lead to liver fibrosis, cirrhosis, and hepatocellular carcinoma. Still, most patients with MASLD die from cardiovascular diseases indicating metabolic alterations related to both liver and cardiovascular pathology. AIMS AND METHODS The aim of this study was to assess biologic pathways behind MASLD progression from steatosis to metabolic dysfunction-associated steatohepatitis (MASH) using non-targeted liquid chromatography-mass spectrometry analysis in 106 severely obese individuals (78 women, mean age 47.7 7 ± 9.2 years, body mass index 41.8 ± 4.3 kg/m²) undergoing laparoscopic Roux-en-Y gastric bypass. RESULTS We identified several metabolites that are associated with MASLD progression. Most importantly, we observed a decrease of lysophosphatidylcholines LPC(18:2), LPC(18:3), and LPC(20:3) and increase of xanthine when comparing those with steatosis to those with MASH. We found that indole propionic acid and threonine were negatively correlated to fibrosis, but not with the metabolic disturbances associated with cardiovascular risk. Xanthine, ketoleucine, and tryptophan were positively correlated to lobular inflammation and ballooning but also with insulin resistance, and dyslipidemia, respectively. The results did not change when taking into account the most important genetic risk factors of MASLD. CONCLUSIONS Our findings suggest that there are several separate biological pathways, some of them independent of insulin resistance and dyslipidemia, associating with MASLD.
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Affiliation(s)
- Ambrin Farizah Babu
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, 70210 Kuopio, Finland
| | - Saana Palomurto
- Department of Surgery, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Vesa Kärjä
- Department of Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Pirjo Käkelä
- Department of Surgery, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, 70211 Kuopio, Finland; LC-MS Metabolomics Center, Biocenter Kuopio, 70211 Kuopio, Finland
| | - Kati Hanhineva
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, 70210 Kuopio, Finland; Department of Life Technologies, Food Sciences Unit, University of Turku, 20014 Turku, Finland
| | - Jussi Pihlajamäki
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, 70210 Kuopio Finland
| | - Ville Männistö
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland.
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13
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Robeyns R, Sisto A, Iturrospe E, da Silva KM, van de Lavoir M, Timmerman V, Covaci A, Stroobants S, van Nuijs ALN. The Metabolic and Lipidomic Fingerprint of Torin1 Exposure in Mouse Embryonic Fibroblasts Using Untargeted Metabolomics. Metabolites 2024; 14:248. [PMID: 38786725 PMCID: PMC11123261 DOI: 10.3390/metabo14050248] [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: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Torin1, a selective kinase inhibitor targeting the mammalian target of rapamycin (mTOR), remains widely used in autophagy research due to its potent autophagy-inducing abilities, regardless of its unspecific properties. Recognizing the impact of mTOR inhibition on metabolism, our objective was to develop a reliable and thorough untargeted metabolomics workflow to study torin1-induced metabolic changes in mouse embryonic fibroblast (MEF) cells. Crucially, our quality assurance and quality control (QA/QC) protocols were designed to increase confidence in the reported findings by reducing the likelihood of false positives, including a validation experiment replicating all experimental steps from sample preparation to data analysis. This study investigated the metabolic fingerprint of torin1 exposure by using liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based untargeted metabolomics platforms. Our workflow identified 67 altered metabolites after torin1 exposure, combining univariate and multivariate statistics and the implementation of a validation experiment. In particular, intracellular ceramides, diglycerides, phosphatidylcholines, phosphatidylethanolamines, glutathione, and 5'-methylthioadenosine were downregulated. Lyso-phosphatidylcholines, lyso-phosphatidylethanolamines, glycerophosphocholine, triglycerides, inosine, and hypoxanthine were upregulated. Further biochemical pathway analyses provided deeper insights into the reported changes. Ultimately, our study provides a valuable workflow that can be implemented for future investigations into the effects of other compounds, including more specific autophagy modulators.
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Affiliation(s)
- Rani Robeyns
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Angela Sisto
- Peripheral Neuropathy Research Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Elias Iturrospe
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | | | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Adrian Covaci
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Sigrid Stroobants
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Antwerp, Belgium
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14
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Gao Y, Zhang G, Jiang S, Liu Y. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. IMETA 2024; 3:e175. [PMID: 38868508 PMCID: PMC10989175 DOI: 10.1002/imt2.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 06/14/2024]
Abstract
The increasing application of meta-omics approaches to investigate the structure, function, and intercellular interactions of microbial communities has led to a surge in available data. However, this abundance of human and environmental microbiome data has exposed new scalability challenges for existing bioinformatics tools. In response, we introduce Wekemo Bioincloud-a specialized platform for -omics studies. This platform offers a comprehensive analysis solution, specifically designed to alleviate the challenges of tool selection for users in the face of expanding data sets. As of now, Wekemo Bioincloud has been regularly equipped with 22 workflows and 65 visualization tools, establishing itself as a user-friendly and widely embraced platform for studying diverse data sets. Additionally, the platform enables the online modification of vector outputs, and the registration-independent personalized dashboard system ensures privacy and traceability. Wekemo Bioincloud is freely available at https://www.bioincloud.tech/.
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Affiliation(s)
- Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Guoxing Zhang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Shunyao Jiang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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15
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Koistinen VM, Haldar S, Tuomainen M, Lehtonen M, Klåvus A, Draper J, Lloyd A, Beckmann M, Bal W, Ross AB, Brandt K, Fawcett L, Seal C, Hanhineva K. Metabolic changes in response to varying whole-grain wheat and rye intake. NPJ Sci Food 2024; 8:8. [PMID: 38291073 PMCID: PMC10828387 DOI: 10.1038/s41538-024-00247-0] [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: 01/27/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
Epidemiological studies have shown associations between whole-grain intake and lowered disease risk. A sufficient level of whole-grain intake to reach the health benefits has not been established, and there is limited knowledge about the impact of whole-grain intake on metabolite levels. In this clinical intervention study, we aimed to identify plasma and urine metabolites associated with two different intake levels of whole-grain wheat and rye and to correlate them with clinical plasma biomarkers. Healthy volunteers (N = 68) were divided into two groups receiving either whole-grain wheat or whole-grain rye in two four-week interventions with 48 and 96 g/d of whole grains consumed. The metabolomics of the plasma samples was performed with UPLC-QTOF-MS. Plasma alkylresorcinols were quantified with GC-MS and plasma and urinary mammalian lignans with HPLC-ECD. The high-dose intervention impacted the metabolite profile, including microbial metabolites, more in the rye-enriched diet compared with wheat. Among the increased metabolites were alkylresorcinol glucuronides, sinapyl alcohol, and pipecolic acid betaine, while the decreased metabolites included acylcarnitines and ether lipids. Plasma alkylresorcinols, urinary enterolactone, and total mammalian lignans reflected the study diets in a dose-dependent manner. Several key metabolites linked with whole-grain consumption and gut microbial metabolism increased in a linear manner between the two interventions. The results reveal that an increase in whole-grain intake, particularly rye, is strongly reflected in the metabolite profile, is correlated with clinical variables, and suggests that a diet rich in whole grains promotes the growth and/or metabolism of microbes producing potentially beneficial microbial metabolites.
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Affiliation(s)
- Ville M Koistinen
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland.
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| | - Sumanto Haldar
- Clinical Nutrition Research Centre, Singapore Institute of Food and Biotechnology Innovations (SIFBI), Yong Loo Lin School of Medicine, Singapore, 117599, Singapore
| | - Marjo Tuomainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - John Draper
- Department of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Amanda Lloyd
- Department of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Manfred Beckmann
- Department of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales, UK
| | - Wendy Bal
- Human Nutrition and Exercise Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Kirsten Brandt
- Human Nutrition and Exercise Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lee Fawcett
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK
| | - Chris Seal
- Human Nutrition and Exercise Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kati Hanhineva
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Food and Nutrition Science Division, Chalmers University of Technology, Gothenburg, Sweden
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16
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Emanuel IB, Cooperstone JL, Hand FP. Ultra-High Performance Liquid Chromatography-Tandem Mass Spectrometry Identification of Metabolites in Winterberry Fruit Putatively Associated with Natural Disease Resistance to Diaporthe ilicicola. PHYTOPATHOLOGY 2024; 114:93-101. [PMID: 37435936 DOI: 10.1094/phyto-04-23-0130-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Winterberry holly (Ilex verticillata) is an ornamental plant popularly used in landscape design and sold as cut branches for fall and winter seasonal decoration. Latent fruit rot of winterberry is an emerging disease caused by the fungus Diaporthe ilicicola, which can result in up to 100% crop loss. Diaporthe ilicicola infects open flowers in spring, but symptom onset does not occur until the end of the growing season when the fruit is fully mature. This study was conducted to identify compounds displaying significant variation in abundance during fruit maturation and that may be putatively associated with natural disease resistance observed when the fruit is immature. Winterberry 'Sparkleberry' fruits collected at four timepoints during the 2018 and 2019 seasons were extracted in methanol and analyzed using high resolution ultra-high performance liquid chromatography-tandem mass spectrometry. The results showed a distinct separation of metabolic profiles based on fruit phenological stage. The top 100 features that were differentially expressed between immature and mature fruit were selected from both electrospray ionization (ESI) (-) and ESI (+) datasets for annotation. Eleven compounds shown to decrease throughout the season included cinnamic acids, a triterpenoid, terpene lactones, stilbene glycosides, a cyanidin glycoside, and a furopyran. Nine compounds shown to accumulate throughout the season included chlorogenic acid derivatives, hydrolysable tannins, flavonoid glycosides, and a triterpene saponin. Future research will further confirm the exact identity of the compounds of interest and determine whether they are biologically active toward D. ilicicola or I. verticillata. The results could inform breeding programs, chemical management programs, and novel antifungal compound development pipelines.
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Affiliation(s)
- Isabel B Emanuel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43201
| | - Jessica L Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43201
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43201
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17
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Iannone V, Babu AF, Lok J, Gómez-Gallego C, D'Auria G, Vazquez-Uribe R, Vaaben TH, Bongers M, Mikkonen S, Vaittinen M, Tikkanen I, Kettunen M, Klåvus A, Sehgal R, Kaminska D, Pihlajamaki J, Hanhineva K, El-Nezami H, Sommer MOA, Kolehmainen M. Changes in liver metabolic pathways demonstrate efficacy of the combined dietary and microbial therapeutic intervention in MASLD mouse model. Mol Metab 2023; 78:101823. [PMID: 37839774 PMCID: PMC10618820 DOI: 10.1016/j.molmet.2023.101823] [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: 08/25/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023] Open
Abstract
OBJECTIVE Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is the most prevalent liver disease globally, yet no therapies are approved. The effects of Escherichia coli Nissle 1917 expressing aldafermin, an engineered analog of the intestinal hormone FGF19, in combination with dietary change were investigated as a potential treatment for MASLD. METHODS MASLD was induced in C57BL/6J male mice by American lifestyle-induced obesity syndrome diet and then switched to a standard chow diet for seven weeks. In addition to the dietary change, the intervention group received genetically engineered E. coli Nissle expressing aldafermin, while control groups received either E. coli Nissle vehicle or no treatment. MASLD-related plasma biomarkers were measured using an automated clinical chemistry analyzer. The liver steatosis was assessed by histology and bioimaging analysis using Fiji (ImageJ) software. The effects of the intervention in the liver were also evaluated by RNA sequencing and liquid-chromatography-based non-targeted metabolomics analysis. Pathway enrichment studies were conducted by integrating the differentially expressed genes from the transcriptomics findings with the metabolites from the metabolomics results using Ingenuity pathway analysis. RESULTS After the intervention, E. coli Nissle expressing aldafermin along with dietary changes reduced body weight, liver steatosis, plasma aspartate aminotransferase, and plasma cholesterol levels compared to the two control groups. The integration of transcriptomics with non-targeted metabolomics analysis revealed the downregulation of amino acid metabolism and related receptor signaling pathways potentially implicated in the reduction of hepatic steatosis and insulin resistance. Moreover, the downregulation of pathways linked to lipid metabolism and changes in amino acid-related pathways suggested an overall reduction of oxidative stress in the liver. CONCLUSIONS These data support the potential for using engineered microbial therapeutics in combination with dietary changes for managing MASLD.
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Affiliation(s)
- Valeria Iannone
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland
| | - Ambrin Farizah Babu
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, 70210 Kuopio, Finland
| | - Johnson Lok
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland
| | - Carlos Gómez-Gallego
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland.
| | - Giuseppe D'Auria
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, FISABIO, 46020 Valencia, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ruben Vazquez-Uribe
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark
| | - Troels Holger Vaaben
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark
| | - Mareike Bongers
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark
| | - Santtu Mikkonen
- University Department of Technical Physics, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maija Vaittinen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland
| | - Ida Tikkanen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland
| | - Mikko Kettunen
- Biomedical Imaging Unit, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Anton Klåvus
- Afekta Technologies Ltd., Microkatu 1, 70210 Kuopio, Finland
| | - Ratika Sehgal
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland
| | - Dorota Kaminska
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland; Department of Medicine, Division of Cardiology, University of California, Los Angeles, CA 90095, USA
| | - Jussi Pihlajamaki
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland; Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Kati Hanhineva
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, 70210 Kuopio, Finland; Department of Life Technologies, Food Sciences Unit, University of Turku, 20014 Turku, Finland
| | - Hani El-Nezami
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland; University of Hong Kong, Hong Kong SAR, Molecular and Cell Biology Research Area, School of Biological Sciences, Hong Kong, Hong Kong, China
| | - Morten Otto Alexander Sommer
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark.
| | - Marjukka Kolehmainen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200 Kuopio, Finland
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18
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Husso A, Pessa-Morikawa T, Koistinen VM, Kärkkäinen O, Kwon HN, Lahti L, Iivanainen A, Hanhineva K, Niku M. Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta. BMC Biol 2023; 21:207. [PMID: 37794486 PMCID: PMC10552303 DOI: 10.1186/s12915-023-01709-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND The maternal microbiota modulates fetal development, but the mechanisms of these earliest host-microbe interactions are unclear. To investigate the developmental impacts of maternal microbial metabolites, we compared full-term fetuses from germ-free and specific pathogen-free mouse dams by gene expression profiling and non-targeted metabolomics. RESULTS In the fetal intestine, critical genes mediating host-microbe interactions, innate immunity, and epithelial barrier were differentially expressed. Interferon and inflammatory signaling genes were downregulated in the intestines and brains of the fetuses from germ-free dams. The expression of genes related to neural system development and function, translation and RNA metabolism, and regulation of energy metabolism were significantly affected. The gene coding for the insulin-degrading enzyme (Ide) was most significantly downregulated in all tissues. In the placenta, genes coding for prolactin and other essential regulators of pregnancy were downregulated in germ-free dams. These impacts on gene expression were strongly associated with microbially modulated metabolite concentrations in the fetal tissues. Aryl sulfates and other aryl hydrocarbon receptor ligands, the trimethylated compounds TMAO and 5-AVAB, Glu-Trp and other dipeptides, fatty acid derivatives, and the tRNA nucleobase queuine were among the compounds strongly associated with gene expression differences. A sex difference was observed in the fetal responses to maternal microbial status: more genes were differentially regulated in male fetuses than in females. CONCLUSIONS The maternal microbiota has a major impact on the developing fetus, with male fetuses potentially more susceptible to microbial modulation. The expression of genes important for the immune system, neurophysiology, translation, and energy metabolism are strongly affected by the maternal microbial status already before birth. These impacts are associated with microbially modulated metabolites. We identified several microbial metabolites which have not been previously observed in this context. Many of the potentially important metabolites remain to be identified.
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Affiliation(s)
- Aleksi Husso
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Pessa-Morikawa
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ville Mikael Koistinen
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Afekta Technologies Ltd., Kuopio, Finland
| | - Olli Kärkkäinen
- Afekta Technologies Ltd., Kuopio, Finland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Hyuk Nam Kwon
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- School of Biological Sciences and Basic-Clinical Convergence Research Institute, University of Ulsan, Ulsan, 44610, South Korea
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Kati Hanhineva
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Afekta Technologies Ltd., Kuopio, Finland
| | - Mikael Niku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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19
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Karpale M, Kummu O, Kärkkäinen O, Lehtonen M, Näpänkangas J, Herfurth UM, Braeuning A, Rysä J, Hakkola J. Pregnane X receptor activation remodels glucose metabolism to promote NAFLD development in obese mice. Mol Metab 2023; 76:101779. [PMID: 37467962 PMCID: PMC10415798 DOI: 10.1016/j.molmet.2023.101779] [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: 03/23/2023] [Revised: 06/14/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023] Open
Abstract
OBJECTIVE Both obesity and exposure to chemicals may induce non-alcoholic fatty liver disease (NAFLD). Pregnane X Receptor (PXR) is a central target of metabolism disrupting chemicals and disturbs hepatic glucose and lipid metabolism. We hypothesized that the metabolic consequences of PXR activation may be modified by existing obesity and associated metabolic dysfunction. METHODS Wildtype and PXR knockout male mice were fed high-fat diet to induce obesity and metabolic dysfunction. PXR was activated with pregnenolone-16α-carbonitrile. Glucose metabolism, hepatosteatosis, insulin signaling, glucose uptake, liver glycogen, plasma and liver metabolomics, and liver, white adipose tissue, and muscle transcriptomics were investigated. RESULTS PXR activation aggravated obesity-induced liver steatosis by promoting lipogenesis and inhibiting fatty acid disposal. Accordingly, hepatic insulin sensitivity was impaired and circulating alanine aminotransferase level increased. Lipid synthesis was facilitated by increased liver glucose uptake and utilization of glycogen reserves resulting in dissociation of hepatosteatosis and hepatic insulin resistance from the systemic glucose tolerance and insulin sensitivity. Furthermore, glucagon-induced hepatic glucose production was impaired. PXR deficiency did not protect from the metabolic manifestations of obesity, but the liver transcriptomics and metabolomics profiling suggest diminished activation of inflammation and less prominent changes in the overall metabolite profile. CONCLUSIONS Obesity and PXR activation by chemical exposure have a synergistic effect on NAFLD development. To support liver fat accumulation the PXR activation reorganizes glucose metabolism that seemingly improves systemic glucose metabolism. This implies that obese individuals, already predisposed to metabolic diseases, may be more susceptible to harmful metabolic effects of PXR-activating drugs and environmental chemicals.
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Affiliation(s)
- Mikko Karpale
- Research Unit of Biomedicine and Internal Medicine, Biocenter Oulu, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Outi Kummu
- Research Unit of Biomedicine and Internal Medicine, Biocenter Oulu, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Juha Näpänkangas
- Department of Pathology, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Uta M Herfurth
- German Federal Institute for Risk Assessment (BfR), Department of Food Safety, Berlin, Germany
| | - Albert Braeuning
- German Federal Institute for Risk Assessment (BfR), Department of Food Safety, Berlin, Germany
| | - Jaana Rysä
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Jukka Hakkola
- Research Unit of Biomedicine and Internal Medicine, Biocenter Oulu, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.
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20
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Alitalo O, González-Hernández G, Rosenholm M, Kohtala P, Matsui N, Müller HK, Theilmann W, Klein A, Kärkkäinen O, Rozov S, Rantamäki T, Kohtala S. Linking Hypothermia and Altered Metabolism with TrkB Activation. ACS Chem Neurosci 2023; 14:3212-3225. [PMID: 37551888 PMCID: PMC10485900 DOI: 10.1021/acschemneuro.3c00350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/13/2023] [Indexed: 08/09/2023] Open
Abstract
Many mechanisms have been proposed to explain acute antidepressant drug-induced activation of TrkB neurotrophin receptors, but several questions remain. In a series of pharmacological experiments, we observed that TrkB activation induced by antidepressants and several other drugs correlated with sedation, and most importantly, coinciding hypothermia. Untargeted metabolomics of pharmacologically dissimilar TrkB activating treatments revealed effects on shared bioenergetic targets involved in adenosine triphosphate (ATP) breakdown and synthesis, demonstrating a common perturbation in metabolic activity. Both activation of TrkB signaling and hypothermia were recapitulated by administration of inhibitors of glucose and lipid metabolism, supporting a close relationship between metabolic inhibition and neurotrophic signaling. Drug-induced TrkB phosphorylation was independent of electroencephalography slow-wave activity and remained unaltered in knock-in mice with the brain-derived neurotrophic factor (BDNF) Val66Met allele, which have impaired activity-dependent BDNF release, alluding to an activation mechanism independent from BDNF and neuronal activity. Instead, we demonstrated that the active maintenance of body temperature prevents activation of TrkB and other targets associated with antidepressants, including p70S6 kinase downstream of the mammalian target of rapamycin (mTOR) and glycogen synthase kinase 3β (GSK3β). Increased TrkB, GSK3β, and p70S6K phosphorylation was also observed during recovery sleep following sleep deprivation, when a physiological temperature drop is known to occur. Our results suggest that the changes in bioenergetics and thermoregulation are causally connected to TrkB activation and may act as physiological regulators of signaling processes involved in neuronal plasticity.
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Affiliation(s)
- Okko Alitalo
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
| | - Gemma González-Hernández
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
| | - Marko Rosenholm
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
- Center
for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Piia Kohtala
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
- Department
of Psychiatry, Weill Cornell Medicine, New York, New York 10021, United States
| | - Nobuaki Matsui
- Faculty
of Pharmacy, Gifu University of Medical
Science, 4-3-3 Nijigaoka,
Kani, Gifu 509-0293, Japan
| | - Heidi Kaastrup Müller
- Translational
Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus N 8200, Denmark
| | - Wiebke Theilmann
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Anders Klein
- Novo
Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark
- Department
of Drug Design & Pharmacology, University
of Copenhagen, Copenhagen DK-2100, Denmark
| | - Olli Kärkkäinen
- School
of Pharmacy, University of Eastern Finland, Kuopio 70210, Finland
- Afekta
Technologies Ltd., Kuopio 70210, Finland
| | - Stanislav Rozov
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
| | - Tomi Rantamäki
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
| | - Samuel Kohtala
- Laboratory
of Neurotherapeutics, Drug Research Program, Division of Pharmacology
and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- SleepWell
Research Program, Faculty of Medicine, University
of Helsinki, Helsinki 00014, Finland
- Department
of Psychiatry, Weill Cornell Medicine, New York, New York 10021, United States
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21
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van de Lavoir M, da Silva KM, Iturrospe E, Robeyns R, van Nuijs ALN, Covaci A. Untargeted hair lipidomics: comprehensive evaluation of the hair-specific lipid signature and considerations for retrospective analysis. Anal Bioanal Chem 2023; 415:5589-5604. [PMID: 37468753 DOI: 10.1007/s00216-023-04851-z] [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: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Lipidomics investigates the composition and function of lipids, typically employing blood or tissue samples as the primary study matrices. Hair has recently emerged as a potential complementary sample type to identify biomarkers in early disease stages and retrospectively document an individual's metabolic status due to its long detection window of up to several months prior to the time of sampling. However, the limited coverage of lipid profiling presented in previous studies has hindered its exploitation. This study aimed to evaluate the lipid coverage of hair using an untargeted liquid chromatography-high-resolution mass spectrometry lipidomics platform. Two distinct three-step exhaustive extraction experiments were performed using a hair metabolomics one-phase extraction technique that has been recently optimized, and the two-phase Folch extraction method which is recognized as the gold standard for lipid extraction in biological matrices. The applied lipidomics workflow improved hair lipid coverage, as only 99 species could be annotated using the one-phase extraction method, while 297 lipid species across six categories were annotated with the Folch method. Several lipids in hair were reported for the first time, including N-acyl amino acids, diradylglycerols, and coenzyme Q10. The study suggests that hair lipids are not solely derived from de novo synthesis in hair, but are also incorporated from sebum and blood, making hair a valuable matrix for clinical, forensic, and dermatological research. The improved understanding of the lipid composition and analytical considerations for retrospective analysis offers valuable insights to contextualize untargeted hair lipidomic analysis and facilitate the use of hair in translational studies.
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Affiliation(s)
- Maria van de Lavoir
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Katyeny Manuela da Silva
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Elias Iturrospe
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Rani Robeyns
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Alexander L N van Nuijs
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Adrian Covaci
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium.
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22
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Hintikka JE, Ahtiainen JP, Permi P, Jalkanen S, Lehtonen M, Pekkala S. Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study. Sci Rep 2023; 13:11228. [PMID: 37433843 DOI: 10.1038/s41598-023-38357-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023] Open
Abstract
Physical activity is essential in weight management, improves overall health, and mitigates obesity-related risk markers. Besides inducing changes in systemic metabolism, habitual exercise may improve gut's microbial diversity and increase the abundance of beneficial taxa in a correlated fashion. Since there is a lack of integrative omics studies on exercise and overweight populations, we studied the metabolomes and gut microbiota associated with programmed exercise in obese individuals. We measured the serum and fecal metabolites of 17 adult women with overweight during a 6-week endurance exercise program. Further, we integrated the exercise-responsive metabolites with variations in the gut microbiome and cardiorespiratory parameters. We found clear correlation with several serum and fecal metabolites, and metabolic pathways, during the exercise period in comparison to the control period, indicating increased lipid oxidation and oxidative stress. Especially, exercise caused co-occurring increase in levels of serum lyso-phosphatidylcholine moieties and fecal glycerophosphocholine. This signature was associated with several microbial metagenome pathways and the abundance of Akkermansia. The study demonstrates that, in the absence of body composition changes, aerobic exercise can induce metabolic shifts that provide substrates for beneficial gut microbiota in overweight individuals.
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Affiliation(s)
- Jukka E Hintikka
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland.
| | - Juha P Ahtiainen
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Sirpa Jalkanen
- MediCity and InFLAMES Flagship, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Marko Lehtonen
- Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Satu Pekkala
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
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23
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Näätänen M, Kårlund A, Mikkonen S, Klåvus A, Savolainen O, Lehtonen M, Karhunen L, Hanhineva K, Kolehmainen M. Metabolic profiles reflect weight loss maintenance and the composition of diet after very-low-energy diet. Clin Nutr 2023; 42:1126-1141. [PMID: 37268538 DOI: 10.1016/j.clnu.2023.05.011] [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: 12/16/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND & AIMS Diet and weight loss affect circulating metabolome. However, metabolite profiles induced by different weight loss maintenance diets and underlying longer term weight loss maintenance remain unknown. Herein, we investigated after-weight-loss metabolic signatures of two isocaloric 24-wk weight maintenance diets differing in satiety value due to dietary fibre, protein and fat contents and identified metabolite features that associated with successful weight loss maintenance. METHODS Non-targeted LC-MS metabolomics approach was used to analyse plasma metabolites of 79 women and men (mean age ± SD 49.7 ± 9.0 years; BMI 34.2 ± 2.5 kg/m2) participating in a weight management study. Participants underwent a 7-week very-low-energy diet (VLED) and were thereafter randomised into two groups for a 24-week weight maintenance phase. Higher satiety food (HSF) group consumed high-fibre, high-protein, and low-fat products, while lower satiety food (LSF) group consumed isocaloric low-fibre products with average protein and fat content as a part of their weight maintenance diets. Plasma metabolites were analysed before the VLED and before and after the weight maintenance phase. Metabolite features discriminating HSF and LSF groups were annotated. We also analysed metabolite features that discriminated participants who maintained ≥10% weight loss (HWM) and participants who maintained <10% weight loss (LWM) at the end of the study, irrespective of the diet. Finally, we assessed robust linear regression between metabolite features and anthropometric and food group variables. RESULTS We annotated 126 metabolites that discriminated the HSF and LSF groups and HWM and LWM groups (p < 0.05). Compared to LSF, the HSF group had lower levels of several amino acids, e.g. glutamine, arginine, and glycine, short-, medium- and long-chain acylcarnitines (CARs), odd- and even-chain lysoglycerophospholipids, and higher levels of fatty amides. Compared to LWM, the HWM group in general showed higher levels of glycerophospholipids with a saturated long-chain and a C20:4 fatty acid tail, and unsaturated free fatty acids (FFAs). Changes in several saturated odd- and even-chain LPCs and LPEs and fatty amides were associated with the intake of many food groups, particularly grain and dairy products. Increase in several (lyso)glycerophospholipids was associated with decrease in body weight and adiposity. Increased short- and medium-chain CARs were related to decreased body fat-free mass. CONCLUSIONS Our results show that isocaloric weight maintenance diets differing in dietary fibre, protein, and fat content affected amino acid and lipid metabolism. Increased abundances of several phospholipid species and FFAs were related with greater weight loss maintenance. Our findings indicate common and distinct metabolites for weight and dietary related variables in the context of weight reduction and weight management. The study was registered in isrctn.org with identifier 67529475.
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Affiliation(s)
- Mari Näätänen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Anna Kårlund
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Department of Life Technologies, Food Sciences Unit, University of Turku, 20014 Turku, Finland.
| | - Santtu Mikkonen
- Department of Applied Physics, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Anton Klåvus
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Otto Savolainen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Department of Biology and Biological Engineering, Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Sweden.
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Leila Karhunen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Kati Hanhineva
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Department of Life Technologies, Food Sciences Unit, University of Turku, 20014 Turku, Finland.
| | - Marjukka Kolehmainen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland.
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24
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Ivanauskaite A, Rantala M, Laihonen L, Konert MM, Schwenner N, Mühlenbeck JS, Finkemeier I, Mulo P. Loss of Chloroplast GNAT Acetyltransferases Results in Distinct Metabolic Phenotypes in Arabidopsis. PLANT & CELL PHYSIOLOGY 2023; 64:549-563. [PMID: 37026998 DOI: 10.1093/pcp/pcad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/16/2023] [Indexed: 05/17/2023]
Abstract
Acetylation is one of the most common chemical modifications found on a variety of molecules ranging from metabolites to proteins. Although numerous chloroplast proteins have been shown to be acetylated, the role of acetylation in the regulation of chloroplast functions has remained mainly enigmatic. The chloroplast acetylation machinery in Arabidopsis thaliana consists of eight General control non-repressible 5 (GCN5)-related N-acetyltransferase (GNAT)-family enzymes that catalyze both N-terminal and lysine acetylation of proteins. Additionally, two plastid GNATs have also been reported to be involved in the biosynthesis of melatonin. Here, we have characterized six plastid GNATs (GNAT1, GNAT2, GNAT4, GNAT6, GNAT7 and GNAT10) using a reverse genetics approach with an emphasis on the metabolomes and photosynthesis of the knock-out plants. Our results reveal the impact of GNAT enzymes on the accumulation of chloroplast-related compounds, such as oxylipins and ascorbate, and the GNAT enzymes also affect the accumulation of amino acids and their derivatives. Specifically, the amount of acetylated arginine and proline was significantly decreased in the gnat2 and gnat7 mutants, respectively, as compared to the wild-type Col-0 plants. Additionally, our results show that the loss of the GNAT enzymes results in increased accumulation of Rubisco and Rubisco activase (RCA) at the thylakoids. Nevertheless, the reallocation of Rubisco and RCA did not have consequent effects on carbon assimilation under the studied conditions. Taken together, our results show that chloroplast GNATs affect diverse aspects of plant metabolism and pave way for future research into the role of protein acetylation.
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Affiliation(s)
- Aiste Ivanauskaite
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Marjaana Rantala
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Laura Laihonen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Minna M Konert
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Naike Schwenner
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Jens S Mühlenbeck
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Paula Mulo
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
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Riquelme G, Bortolotto EE, Dombald M, Monge ME. Model-driven data curation pipeline for LC-MS-based untargeted metabolomics. Metabolomics 2023; 19:15. [PMID: 36856823 DOI: 10.1007/s11306-023-01976-1] [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: 12/05/2022] [Accepted: 01/23/2023] [Indexed: 03/02/2023]
Abstract
INTRODUCTION There is still no community consensus regarding strategies for data quality review in liquid chromatography mass spectrometry (LC-MS)-based untargeted metabolomics. Assessing the analytical robustness of data, which is relevant for inter-laboratory comparisons and reproducibility, remains a challenge despite the wide variety of tools available for data processing. OBJECTIVES The aim of this study was to provide a model to describe the sources of variation in LC-MS-based untargeted metabolomics measurements, to use it to build a comprehensive curation pipeline, and to provide quality assessment tools for data quality review. METHODS Human serum samples (n=392) were analyzed by ultraperformance liquid chromatography coupled to high-resolution mass spectrometry (UPLC-HRMS) using an untargeted metabolomics approach. The pipeline and tools used to process this dataset were implemented as part of the open source, publicly available TidyMS Python-based package. RESULTS The model was applied to understand data curation practices used by the metabolomics community. Sources of variation, which are often overlooked in untargeted metabolomic studies, were identified in the analysis. New tools were used to characterize certain types of variations. CONCLUSION The developed pipeline allowed confirming data robustness by comparing the experimental results with expected values predicted by the model. New quality control practices were introduced to assess the analytical quality of data.
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Affiliation(s)
- Gabriel Riquelme
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA, Ciudad de Buenos Aires, Argentina
| | - Emmanuel Ezequiel Bortolotto
- Laboratorio Central, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199, Ciudad de Buenos Aires, Argentina
| | - Matías Dombald
- Laboratorio Central, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199, Ciudad de Buenos Aires, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina.
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Iannone V, Lok J, Babu AF, Gómez-Gallego C, Willman RM, Koistinen VM, Klåvus A, Kettunen MI, Kårlund A, Schwab U, Hanhineva K, Kolehmainen M, El-Nezami H. Associations of altered hepatic gene expression in American lifestyle-induced obesity syndrome diet-fed mice with metabolic changes during NAFLD development and progression. J Nutr Biochem 2023; 115:109307. [PMID: 36868506 DOI: 10.1016/j.jnutbio.2023.109307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) pathogenesis remains poorly understood due to the complex metabolic and inflammatory changes in the liver. This study aimed to elucidate hepatic events related to inflammation and lipid metabolism and their linkage with metabolic alterations during NAFLD in American lifestyle-induced obesity syndrome (ALIOS) diet-fed mice. Forty-eight C57BL/6J male mice were fed with ALIOS diet (n=24) or control chow diet (n=24) for 8, 12, and 16 weeks. At the end of each timepoint, eight mice were sacrificed where plasma and liver were collected. Hepatic fat accumulation was followed using magnetic resonance imaging and confirmed with histology. Further, targeted gene expression and non-targeted metabolomics analysis were conducted. Our results showed higher hepatic steatosis, body weight, energy consumption, and liver mass in ALIOS diet-fed mice compared to control mice. ALIOS diet altered expression of genes related to inflammation (Tnfa and IL-6) and lipid metabolism (Cd36, Fasn, Scd1, Cpt1a, and Ppara). Metabolomics analysis indicated decrease of lipids containing polyunsaturated fatty acids such as LPE(20:5) and LPC(20:5) with increase of other lipid species such as LPI(16:0) and LPC(16:2) and peptides such as alanyl-phenylalanine and glutamyl-arginine. We further observed novel correlations between different metabolites including sphingolipid, lysophospholipids, peptides, and bile acid with inflammation, lipid uptake and synthesis. Together with the reduction of antioxidant metabolites and gut microbiota-derived metabolites contribute to NAFLD development and progression. The combination of non-targeted metabolomics with gene expression in future studies can further identify key metabolic routes during NAFLD which could be the targets of potential novel therapeutics.
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Affiliation(s)
- Valeria Iannone
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Johnson Lok
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Ambrin Farizah Babu
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Afekta Technologies Ltd., Kuopio, Finland
| | - Carlos Gómez-Gallego
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Roosa Maria Willman
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Mikael Koistinen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Afekta Technologies Ltd., Kuopio, Finland; Department of Life technologies, Food Sciences Unit, University of Turku, Turku, Finland
| | | | - Mikko I Kettunen
- Kuopio Biomedical Imaging Unit, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anna Kårlund
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Ursula Schwab
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Kati Hanhineva
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Afekta Technologies Ltd., Kuopio, Finland; Department of Life technologies, Food Sciences Unit, University of Turku, Turku, Finland.
| | - Marjukka Kolehmainen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| | - Hani El-Nezami
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Molecular and Cell Biology Division, School of Biological Sciences, University of Hong Kong, Hong Kong China
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Identification of Gut Microbial Lysine and Histidine Degradation and CYP-Dependent Metabolites as Biomarkers of Fatty Liver Disease. mBio 2023; 14:e0266322. [PMID: 36715540 PMCID: PMC9973343 DOI: 10.1128/mbio.02663-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Numerous studies have described specific metabolites as biomarkers of severe liver diseases, but very few have measured gut microbiota (GM)-produced metabolites in fatty liver disease. We aimed at finding GM signatures and metabolite markers in plasma and feces related to high liver fat content. Based on imaging, we divided study participants into low (<5%, LF, n = 25) and high (>5%, HF, n = 39) liver fat groups. Fecal (LF n = 14, HF n = 25) and plasma (LF n = 11, HF n = 7) metabolomes of subsets of participants were studied using liquid chromatography/high resolution mass spectrometry. The GM were analyzed using 16S rRNA gene sequencing. Additionally, blood clinical variables and diet were studied. Dyslipidemia, higher liver enzymes and insulin resistance characterized the HF group. No major differences in diet were found between the groups. In the GM, the HF group had lower abundance of Bacteroides and Prevotellaceae NK3B31 group than the LF group after adjusting for metformin use or obesity. In feces, the HF group had higher levels of lysine and histidine degradation products, while 6-hydroxybetatestosterone (metabolized by CYP3A4) was low. Higher plasma levels of caffeine and its metabolites in the HF group indicate that the activity of hepatic CYP1A2 was lower than in the LF group. Our results suggest, that low fecal Prevotellaceae NK3B31 and Bacteroides abundance, and increased lysine and histidine degradation may serve as GM biomarkers of high liver fat. Altered plasma caffeine metabolites and lowered testosterone metabolism may specify decreased CYP activities, and their potential utility, as biomarkers of fatty liver disease. IMPORTANCE Because the high prevalence of nonalcoholic fatty liver disease sets diagnostic challenges to health care, identification of new biomarkers of the disease that in the future could have potential utility as diagnostic biomarkers of high liver fat content is important. Our results show that increased amino acid degradation products in the feces may be such biomarkers. In the blood, molecules that indicate defective hepatic metabolic enzyme activities were identified in individuals with high liver fat content.
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Iturrospe E, Robeyns R, da Silva KM, van de Lavoir M, Boeckmans J, Vanhaecke T, van Nuijs ALN, Covaci A. Metabolic signature of HepaRG cells exposed to ethanol and tumor necrosis factor alpha to study alcoholic steatohepatitis by LC-MS-based untargeted metabolomics. Arch Toxicol 2023; 97:1335-1353. [PMID: 36826472 DOI: 10.1007/s00204-023-03470-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023]
Abstract
Despite the high prevalence of alcoholic liver disease, its identification and characterization remain poor, especially in early stages such as alcoholic fatty liver disease and alcoholic steatohepatitis. This latter implies diagnostic difficulties, few therapeutic options and unclear mechanisms of action. To elucidate the metabolic alterations and pinpoint affected biochemical pathways, alcoholic steatohepatitis was simulated in vitro by exposing HepaRG cells to ethanol (IC10, 368 mM) and tumor necrosis factor alpha (TNF-α, 50 ng/mL) for 24 h. This combined exposure was compared to solely ethanol-exposed as well as -nonexposed cells. Four different metabolomics platforms were used combining liquid chromatography, high-resolution mass spectrometry and drift tube ion mobility to elucidate both intracellular and extracellular metabolic alterations. Some of the key findings include the influence of TNF-α in the upregulation of hepatic triglycerides and the downregulation of hepatic phosphatidylethanolamines and phosphatidylcholines. S-Adenosylmethionine showed to play a central role in the progression of alcoholic steatohepatitis. In addition, fatty acyl esters of hydroxy fatty acid (FAHFA)-containing triglycerides were detected for the first time in human hepatocytes and their alterations showed a potentially important role during the progression of alcoholic steatohepatitis. Ethoxylated phosphorylcholine was identified as a potential new biomarker of ethanol exposure.
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Affiliation(s)
- Elias Iturrospe
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Jette, Belgium.
| | - Rani Robeyns
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | | | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Jette, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Jette, Belgium
| | | | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
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Puris E, Saveleva L, de Sousa Maciel I, Kanninen KM, Auriola S, Fricker G. Protein Expression of Amino Acid Transporters Is Altered in Isolated Cerebral Microvessels of 5xFAD Mouse Model of Alzheimer's Disease. Mol Neurobiol 2023; 60:732-748. [PMID: 36367657 PMCID: PMC9849299 DOI: 10.1007/s12035-022-03111-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Membrane transporters such as ATP-binding cassette (ABC) and solute carrier (SLC) transporters expressed at the neurovascular unit (NVU) play an important role in drug delivery to the brain and have been demonstrated to be involved in Alzheimer's disease (AD) pathogenesis. However, our knowledge of quantitative changes in transporter absolute protein expression and functionality in vivo in NVU in AD patients and animal models is limited. The study aim was to investigate alterations in protein expression of ABC and SLC transporters in the isolated brain microvessels and brain prefrontal cortices of a widely used model of familial AD, 5xFAD mice (8 months old), using a sensitive liquid chromatography tandem mass spectrometry-based quantitative targeted absolute proteomic approach. Moreover, we examined alterations in brain prefrontal cortical and plasmatic levels of transporter substrates in 5xFAD mice compared to age-matched wild-type (WT) controls. ASCT1 (encoded by Slc1a4) protein expression in the isolated brain microvessels and brain prefrontal cortices of 5xFAD mice was twice higher compared to WT controls (p = 0.01). Brain cortical levels of ASCT1 substrate, serine, were increased in 5xFAD mice compared to WT animals. LAT1 (encoded by Slc7a5) and 4F2hc (encoded by Slc3a2) protein expressions were significantly altered in the isolated brain microvessels of 5xFAD mice compared to WT controls (p = 0.008 and p = 0.05, respectively). Overall, the study provides important information, which is crucial for the optimal use of the 5xFAD mouse model in AD drug development and for investigating novel drug delivery approaches. In addition, the findings of the study shed light on the novel potential mechanisms underlying AD pathogenesis.
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Affiliation(s)
- Elena Puris
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
| | - Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Izaque de Sousa Maciel
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Gert Fricker
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
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Yu J, Sun H, Yang Y, Yan Y. Sesamolin Alleviates Nonalcoholic Fatty Liver Disease through Modulating Gut Microbiota and Metabolites in High-Fat and High-Fructose Diet-Fed Mice. Int J Mol Sci 2022; 23:ijms232213853. [PMID: 36430326 PMCID: PMC9694049 DOI: 10.3390/ijms232213853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become a major public health problem. The effects of sesamolin on obesity-associated NAFLD and its possible mechanism are still poorly understood. The present study investigated the effects of sesamolin on NAFLD and changes in gut microbiota and serum metabolites in high-fat and high-fructose (HF-HF) diet-fed mice. Mice with NAFLD were treated with or without sesamolin. Sesamolin effectively suppressed obesity-associated metabolic disorder, attenuated hepatic steatosis and the infiltration of inflammatory cells, and decreased levels of hepatic proinflammatory cytokines. Sesamolin also altered the composition of gut microbiota at the genus level. Additionally, differential serum metabolite biomarkers identified in an untargeted metabolomics analysis showed that sesamolin changed the levels of metabolites and influenced metabolomics pathways including caffeine metabolism, steroid hormone biosynthesis, and cysteine and methionine metabolism. Changes in metabolite biomarkers and the abundances of Faecalibaculum, Lachnoclostridium, Mucispirillum, Allobaculum, and Bacteroides are highly correlated with those factors involved in the progression of NAFLD. These results are important in deciphering new mechanisms by which changes in bacteria and metabolites in sesamolin treatment might be associated with the alleviation of obesity-associated NAFLD in HF-HF diet-fed mice. Thus, sesamolin may be a potential compound for obesity-associated NAFLD treatment.
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Comprehensive Steroid Assay with Non-Targeted Analysis Using Liquid Chromatography Ion Mobility Mass Spectrometry. Int J Mol Sci 2022; 23:ijms232213858. [PMID: 36430339 PMCID: PMC9697045 DOI: 10.3390/ijms232213858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Aldosterone-producing adenomas (APAs) have different steroid profiles in serum, depending on the causative genetic mutation. Ion mobility is a separation technique for gas-phase ions based on their m/z values, shapes, and sizes. Human serum (100 µL) was purified by liquid-liquid extraction using tert-butyl methyl ether/ethyl acetate at 1/1 (v/v) and mixed with deuterium-labeled steroids as the internal standard. The separated supernatant was dried, re-dissolved in water containing 20% methanol, and injected into a liquid chromatography-ion mobility-mass spectrometer (LC/IM/MS). We established a highly sensitive assay system by separating 20 steroids based on their retention time, m/z value, and drift time. Twenty steroids were measured in the serum of patients with primary aldosteronism, essential hypertension, and healthy subjects and were clearly classified using principal component analysis. This method was also able to detect phosphatidylcholine and phosphatidylethanolamine, which were not targeted. LC/IM/MS has a high selectivity for known compounds and has the potential to provide information on unknown compounds. This analytical method has the potential to elucidate the pathogenesis of APA and identify unknown steroids that could serve as biomarkers for APA with different genetic mutations.
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Algera JP, Magnusson MK, Öhman L, Störsrud S, Simrén M, Törnblom H. Randomised controlled trial: effects of gluten-free diet on symptoms and the gut microenvironment in irritable bowel syndrome. Aliment Pharmacol Ther 2022; 56:1318-1327. [PMID: 36173041 PMCID: PMC9828804 DOI: 10.1111/apt.17239] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/05/2022] [Accepted: 09/17/2022] [Indexed: 01/30/2023]
Abstract
BACKGROUND A gluten-free diet reduces symptoms in some patients with irritable bowel syndrome (IBS) through unclear mechanisms. AIMS To assess the effects of gluten-free versus gluten-containing diet on symptoms and the gut microenvironment, and to identify predictors of response to the gluten-free diet in IBS METHODS: Twenty patients with IBS and 18 healthy controls (HC) followed a gluten-free diet during two 14-day intervention periods where they sprinkled either gluten (14 g/day) or rice flour powder over their meals. Primary outcomes included effects of the interventions on IBS symptoms (IBS-SSS) and bowel habits. Secondary outcomes included effects of gluten-free diet on faecal microbiota and metabolite profile. RESULTS IBS symptoms improved during the gluten-free (p = 0.02), but not the gluten-containing period, with no difference between the interventions. IBS patients reported fewer loose stools during the gluten-free intervention (p = 0.01). Patients with IBS and HC presented distinct metabolite profiles based on the effects of the gluten-free diet (p < 0.001). True responders (reduced IBS-SSS by ≥50 solely after gluten-free period) and non-responders were discriminated based on the effects of the gluten-free diet on the microbiota (p < 0.01) and metabolite profiles (p < 0.001). The response to the gluten-free diet could be predicted by the metabolite profile before the intervention (p < 0.001). CONCLUSIONS A gluten-free diet may influence symptoms in a subset of patients with IBS, with a particular effect on bowel habits. A gluten-free diet seems to impact the gut microenvironment. Responsiveness to the gluten-free diet may be predicted by the metabolite profile. CLINICALTRIALS gov: NCT03869359.
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Affiliation(s)
- Joost P. Algera
- Department of Molecular and Clinical MedicineInstitute of MedicineUniversity of GothenburgGothenburgSweden
| | - Maria K. Magnusson
- Department of Microbiology and ImmunologyInstitute of BiomedicineUniversity of GothenburgGothenburgSweden
| | - Lena Öhman
- Department of Microbiology and ImmunologyInstitute of BiomedicineUniversity of GothenburgGothenburgSweden
| | - Stine Störsrud
- Department of Molecular and Clinical MedicineInstitute of MedicineUniversity of GothenburgGothenburgSweden
| | - Magnus Simrén
- Department of Molecular and Clinical MedicineInstitute of MedicineUniversity of GothenburgGothenburgSweden,Center for Functional Gastrointestinal and Motility DisordersUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Hans Törnblom
- Department of Molecular and Clinical MedicineInstitute of MedicineUniversity of GothenburgGothenburgSweden
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Koistinen VM, Hedberg M, Shi L, Johansson A, Savolainen O, Lehtonen M, Aura A, Hanhineva K, Landberg R. Metabolite Pattern Derived from Lactiplantibacillus plantarum-Fermented Rye Foods and In Vitro Gut Fermentation Synergistically Inhibits Bacterial Growth. Mol Nutr Food Res 2022; 66:e2101096. [PMID: 35960594 PMCID: PMC9787878 DOI: 10.1002/mnfr.202101096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/30/2022] [Indexed: 12/30/2022]
Abstract
SCOPE Fermentation improves many food characteristics using microbes, such as lactic acid bacteria (LAB). Recent studies suggest fermentation may also enhance the health properties, but mechanistic evidence is lacking. The study aims to identify a metabolite pattern reproducibly produced during sourdough and in vitro colonic fermentation of various whole-grain rye products and how it affects the growth of bacterial species of potential importance to health and disease. METHODS AND RESULTS The study uses Lactiplantibacillus plantarum DSMZ 13890 strain, previously shown to favor rye as its substrate. Using LC-MS metabolomics, the study finds seven microbial metabolites commonly produced during the fermentations, including dihydroferulic acid, dihydrocaffeic acid, and five amino acid metabolites, and stronger inhibition is achieved when exposing the bacteria to a mixture of the metabolites in vitro compared to individual compound exposures. CONCLUSION The study suggests that metabolites produced by LAB may synergistically modulate the local microbial ecology, such as in the gut. This could provide new hypotheses on how fermented foods influence human health via diet-microbiota interactions.
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Affiliation(s)
- Ville M. Koistinen
- Institute of Public Health and Clinical NutritionUniversity of Eastern FinlandKuopio70211Finland,Food Chemistry and Food Development Unit, Department of BiochemistryUniversity of TurkuTurkuTurku20014Finland,Afekta Technologies Ltd.Kuopio70210Finland
| | - Maria Hedberg
- Department of Odontology/Oral MicrobiologyUmeå UniversityUmeå90187Sweden
| | - Lin Shi
- Division of Food and Nutrition Science, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg41296Sweden,College of Food Engineering and Nutritional ScienceShaanxi Normal UniversityXi'an710119China
| | - Anders Johansson
- Department of Odontology/Oral MicrobiologyUmeå UniversityUmeå90187Sweden
| | - Otto Savolainen
- Institute of Public Health and Clinical NutritionUniversity of Eastern FinlandKuopio70211Finland,Division of Food and Nutrition Science, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg41296Sweden
| | - Marko Lehtonen
- School of PharmacyUniversity of Eastern FinlandKuopio70211Finland
| | - Anna‐Marja Aura
- VTT Technical Research Centre of Finland Ltd.Espoo02044Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical NutritionUniversity of Eastern FinlandKuopio70211Finland,Food Chemistry and Food Development Unit, Department of BiochemistryUniversity of TurkuTurkuTurku20014Finland,Division of Food and Nutrition Science, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg41296Sweden
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg41296Sweden
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34
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Iribarren C, Nordlander S, Sundin J, Isaksson S, Savolainen O, Törnblom H, Magnusson MK, Simrén M, Öhman L. Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids. Neurogastroenterol Motil 2022; 34:e14390. [PMID: 35485994 PMCID: PMC9786662 DOI: 10.1111/nmo.14390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Alteration of the host-microbiota cross talk at the intestinal barrier may participate in the pathophysiology of irritable bowel syndrome (IBS). Therefore, we aimed to determine effects of fecal luminal factors from IBS patients on the colonic epithelium using colonoids. METHODS Colon-derived organoid monolayers, colonoids, generated from a healthy subject, underwent stimulation with fecal supernatants from healthy subjects and IBS patients with predominant diarrhea, phosphate-buffered saline (PBS), or lipopolysaccharide (LPS). Cytokines in cell cultures and fecal LPS were measured by ELISA and mRNA gene expression of monolayers was analyzed using Qiagen RT2 Profiler PCR Arrays. The fecal microbiota profile was determined by the GA-map™ dysbiosis test and the fecal metabolite profile was analyzed by untargeted liquid chromatography/mass spectrometry. KEY RESULTS Colonoid monolayers stimulated with fecal supernatants from healthy subjects (n = 7), PBS (n = 4) or LPS (n = 3) presented distinct gene expression profiles, with some overlap (R2 Y = 0.70, Q2 = 0.43). Addition of fecal supernatants from healthy subjects and IBS patients (n = 9) gave rise to different gene expression profiles of the colonoid monolayers (R2 Y = 0.79, Q2 = 0.64). Genes (n = 22) related to immune response (CD1D, TLR5) and barrier integrity (CLDN15, DSC2) contributed to the separation. Levels of proinflammatory cytokines in colonoid monolayer cultures were comparable when stimulated with fecal supernatants from either donor types. Fecal microbiota and metabolite profiles, but not LPS content, differed between the study groups. CONCLUSIONS Fecal luminal factors from IBS patients induce a distinct colonic epithelial gene expression, potentially reflecting the disease pathophysiology. The culture of colonoids from healthy subjects with fecal supernatants from IBS patients may facilitate the exploration of IBS related intestinal micro-environmental and barrier interactions.
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Affiliation(s)
- Cristina Iribarren
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Sofia Nordlander
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Johanna Sundin
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Stefan Isaksson
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry InfrastructureDepartment of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Hans Törnblom
- Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Maria K. Magnusson
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Magnus Simrén
- Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Center for Functional GI and Motility DisordersUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Lena Öhman
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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35
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Haikonen R, Kärkkäinen O, Koistinen V, Hanhineva K. Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease. Trends Endocrinol Metab 2022; 33:463-480. [PMID: 35508517 DOI: 10.1016/j.tem.2022.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 12/01/2022]
Abstract
5-Aminovaleric acid betaine (5-AVAB) is a trimethylated compound associated with the gut microbiota, potentially produced endogenously, and related to the dietary intake of certain foods such as whole grains. 5-AVAB accumulates within the metabolically active tissues and has been typically found in higher concentrations in the heart, muscle, and brown adipose tissue. Furthermore, 5-AVAB has been associated with positive health effects such as fetal brain development, insulin secretion, and reduced cancer risk. However, it also has been linked with some negative health outcomes such as cardiovascular disease and fatty liver disease. At the cellular level, 5-AVAB can influence cellular energy metabolism by reducing β-oxidation of fatty acids. This review will focus on the metabolic role of 5-AVAB with respect to both physiology and pathology. Moreover, the analytics and origin of 5-AVAB and related compounds will be reviewed.
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Affiliation(s)
- Retu Haikonen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| | - Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Ville Koistinen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Life Technologies, Food Chemistry and Food Development Unit, University of Turku, Turku, Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Life Technologies, Food Chemistry and Food Development Unit, University of Turku, Turku, Finland; Department of Biology and Biological Engineering, Division of Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
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36
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da Silva KM, Iturrospe E, van den Boom R, van de Lavoir M, Robeyns R, Vergauwen L, Knapen D, Cuykx M, Covaci A, van Nuijs ALN. Lipidomics profiling of zebrafish liver through untargeted liquid chromatography-high resolution mass spectrometry. J Sep Sci 2022; 45:2935-2945. [PMID: 35716100 DOI: 10.1002/jssc.202200214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022]
Abstract
Lipidomics analysis of zebrafish tissues has shown promising results to understand disease-related outcomes of exposure to toxic substances at molecular level. However, knowledge about their lipidome is limited, as most untargeted studies only identify the lipids that are statistically significant in their setup. In this work, liquid chromatography-high resolution mass spectrometry was used to study different aspects of the analytical workflow, i.e., extraction solvents (methanol/chloroform/water (3/2/2, v/v/v), methanol/dichloromethane/water (2/3/2, v/v/v) and methanol/methyl-tert-butyl ether/water (3/10/2.5, v/v/v), instrumental response, and strategies used for lipid annotation. The number of high-quality features (relative standard deviation of the intensity values ≤ 10% in the range 103 -107 counts) was affected by the dilution of lipid extracts, indicating that it is an important parameter for developing untargeted methods. The workflows used allowed the selection of a dilution factor to annotate 712 lipid species (507 bulk lipids) in zebrafish liver using four software (LipidMatch, LipidHunter, MS-DIAL and Lipostar). Retention time mapping was a valuable tool to filter lipid annotations obtained from automatic software annotations. The lipid profiling of zebrafish livers will help in a better understanding of the true constitution of their lipidome at the species level, as well as in the use of zebrafish in toxicological studies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Katyeny Manuela da Silva
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Elias Iturrospe
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium.,Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Campus Jette, Vrije Universiteit Brussels, Laarbeeklaan 103, Brussels, 1090, Belgium
| | - Rik van den Boom
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Maria van de Lavoir
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Rani Robeyns
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Lucia Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Matthias Cuykx
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium.,Department of Laboratory Medicine AZ Turnhout, Rubenslaan 166, Turnhout, 2300, Belgium
| | - Adrian Covaci
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Alexander L N van Nuijs
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
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Babu AF, Csader S, Männistö V, Tauriainen MM, Pentikäinen H, Savonen K, Klåvus A, Koistinen V, Hanhineva K, Schwab U. Effects of exercise on NAFLD using non-targeted metabolomics in adipose tissue, plasma, urine, and stool. Sci Rep 2022; 12:6485. [PMID: 35444259 PMCID: PMC9019539 DOI: 10.1038/s41598-022-10481-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/01/2022] [Indexed: 02/08/2023] Open
Abstract
The mechanisms by which exercise benefits patients with non-alcoholic fatty liver disease (NAFLD), the most common liver disease worldwide, remain poorly understood. A non-targeted liquid chromatography-mass spectrometry (LC–MS)-based metabolomics analysis was used to identify metabolic changes associated with NAFLD in humans upon exercise intervention (without diet change) across four different sample types—adipose tissue (AT), plasma, urine, and stool. Altogether, 46 subjects with NAFLD participated in this randomized controlled intervention study. The intervention group (n = 21) performed high-intensity interval training (HIIT) for 12 weeks while the control group (n = 25) kept their sedentary lifestyle. The participants' clinical parameters and metabolic profiles were compared between baseline and endpoint. HIIT significantly decreased fasting plasma glucose concentration (p = 0.027) and waist circumference (p = 0.028); and increased maximum oxygen consumption rate and maximum achieved workload (p < 0.001). HIIT resulted in sample-type-specific metabolite changes, including accumulation of amino acids and their derivatives in AT and plasma, while decreasing in urine and stool. Moreover, many of the metabolite level changes especially in the AT were correlated with the clinical parameters monitored during the intervention. In addition, certain lipids increased in plasma and decreased in the stool. Glyco-conjugated bile acids decreased in AT and urine. The 12-week HIIT exercise intervention has beneficial ameliorating effects in NAFLD subjects on a whole-body level, even without dietary changes and weight loss. The metabolomics analysis applied to the four different sample matrices provided an overall view on several metabolic pathways that had tissue-type specific changes after HIIT intervention in subjects with NAFLD. The results highlight especially the role of AT in responding to the HIIT challenge, and suggest that altered amino acid metabolism in AT might play a critical role in e.g. improving fasting plasma glucose concentration. Trial registration ClinicalTrials.gov (NCT03995056).
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Affiliation(s)
- Ambrin Farizah Babu
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210, Kuopio, Finland.,Afekta Technologies Ltd., Yliopistonranta 1L, 70211, Kuopio, Finland
| | - Susanne Csader
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210, Kuopio, Finland
| | - Ville Männistö
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Milla-Maria Tauriainen
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210, Kuopio, Finland.,Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Kai Savonen
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland.,Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Anton Klåvus
- Afekta Technologies Ltd., Yliopistonranta 1L, 70211, Kuopio, Finland
| | - Ville Koistinen
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210, Kuopio, Finland.,Afekta Technologies Ltd., Yliopistonranta 1L, 70211, Kuopio, Finland.,Department of Life Technologies, Food Chemistry and Food Development Unit, University of Turku, 20014, Turku, Finland
| | - Kati Hanhineva
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210, Kuopio, Finland.,Afekta Technologies Ltd., Yliopistonranta 1L, 70211, Kuopio, Finland.,Department of Life Technologies, Food Chemistry and Food Development Unit, University of Turku, 20014, Turku, Finland
| | - Ursula Schwab
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210, Kuopio, Finland. .,Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland.
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Rangel-Huerta OD, de la Torre-Aguilar MJ, Mesa MD, Flores-Rojas K, Pérez-Navero JL, Baena-Gómez MA, Gil A, Gil-Campos M. The Metabolic Impact of Two Different Parenteral Nutrition Lipid Emulsions in Children after Hematopoietic Stem Cell Transplantation: A Lipidomics Investigation. Int J Mol Sci 2022; 23:3667. [PMID: 35409026 PMCID: PMC8998446 DOI: 10.3390/ijms23073667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) involves the infusion of either bone marrow or blood cells preceded by toxic chemotherapy. However, there is little knowledge about the clinical benefits of parenteral nutrition (PN) in patients receiving high-dose chemotherapy during HSCT. We investigated the lipidomic profile of plasma and the targeted fatty acid profiles of plasma and erythrocytes in children after HSCT using PN with either a fish oil-based lipid emulsion or a classic soybean oil emulsion. An untargeted liquid chromatography high-resolution mass spectrometry platform connected with a novel in silico annotation algorithm was utilized to determine the most relevant chemical subclasses affected. In addition, we explored the interrelation between the lipidomics profile in plasma, the targeted fatty acid profile in plasma and erythrocytes, several biomarkers of inflammation, and antioxidant defense using an innovative data integration analysis based on Latent Components. We observed that the fish oil-based lipid emulsion had an impact in several lipid subclasses, mainly glycerophosphocholines (PC), glycerophosphoserines (PS), glycerophosphoethanolamines (PE), oxidized PE (O-PE), 1-alkyl,2-acyl PS, lysophosphatidylethanolamines (LPE), oxidized PS (O-PS) and dicarboxylic acids. In contrast, the classic soybean oil emulsion did not. Several connections across the different blocks of data were found and aid in interpreting the impact of the lipid emulsions on metabolic health.
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Affiliation(s)
| | - María José de la Torre-Aguilar
- Department of Pediatrics, Unit of Pediatric Research, Reina Sofia University Hospital, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), University of Córdoba, Avda Menéndez Pidal s/n, 14004 Cordoba, Spain; (M.J.d.l.T.-A.); (K.F.-R.); (J.L.P.-N.); (M.A.B.-G.); (M.G.-C.)
| | - María Dolores Mesa
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, 18016 Armilla, Spain;
- Instituto de Investigación Biosanitaria ibs.Granada, 18012 Granada, Spain
| | - Katherine Flores-Rojas
- Department of Pediatrics, Unit of Pediatric Research, Reina Sofia University Hospital, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), University of Córdoba, Avda Menéndez Pidal s/n, 14004 Cordoba, Spain; (M.J.d.l.T.-A.); (K.F.-R.); (J.L.P.-N.); (M.A.B.-G.); (M.G.-C.)
| | - Juan Luis Pérez-Navero
- Department of Pediatrics, Unit of Pediatric Research, Reina Sofia University Hospital, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), University of Córdoba, Avda Menéndez Pidal s/n, 14004 Cordoba, Spain; (M.J.d.l.T.-A.); (K.F.-R.); (J.L.P.-N.); (M.A.B.-G.); (M.G.-C.)
| | - María Auxiliadora Baena-Gómez
- Department of Pediatrics, Unit of Pediatric Research, Reina Sofia University Hospital, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), University of Córdoba, Avda Menéndez Pidal s/n, 14004 Cordoba, Spain; (M.J.d.l.T.-A.); (K.F.-R.); (J.L.P.-N.); (M.A.B.-G.); (M.G.-C.)
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, 18016 Armilla, Spain;
- Instituto de Investigación Biosanitaria ibs.Granada, 18012 Granada, Spain
| | - Mercedes Gil-Campos
- Department of Pediatrics, Unit of Pediatric Research, Reina Sofia University Hospital, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), University of Córdoba, Avda Menéndez Pidal s/n, 14004 Cordoba, Spain; (M.J.d.l.T.-A.); (K.F.-R.); (J.L.P.-N.); (M.A.B.-G.); (M.G.-C.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
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39
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Iturrospe E, da Silva KM, Robeyns R, van de Lavoir M, Boeckmans J, Vanhaecke T, van Nuijs ALN, Covaci A. Metabolic Signature of Ethanol-Induced Hepatotoxicity in HepaRG Cells by Liquid Chromatography-Mass Spectrometry-Based Untargeted Metabolomics. J Proteome Res 2022; 21:1153-1166. [PMID: 35274962 DOI: 10.1021/acs.jproteome.2c00029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alcoholic liver disease is highly prevalent but poorly identified and characterized, leading to knowledge gaps, which impairs early diagnosis. Excessive alcohol consumption is known to alter lipid metabolism, followed by progressive intracellular lipid accumulation, resulting in alcoholic fatty liver disease. In this study, HepaRG cells were exposed to ethanol at IC10 and 1/10 IC10 for 24 and 48 h. Metabolic alterations were investigated intra- and extracellularly with liquid chromatography-high-resolution mass spectrometry. Ion mobility was added as an extra separation dimension for untargeted lipidomics to improve annotation confidence. Distinctive patterns between exposed and control cells were consistently observed, with intracellular upregulation of di- and triglycerides, downregulation of phosphatidylcholines and phosphatidylethanolamines, sphingomyelins, and S-adenosylmethionine, among others. Several intracellular metabolic patterns could be related to changes in the extracellular environment, such as increased intracellular hydrolysis of sphingomyelins, leading to increased phosphorylcholine secretion. Carnitines showed alterations depending on the size of their carbon chain, which highlights the interplay between β-oxidation in mitochondria and peroxisomes. Potential new biomarkers of ethanol-induced hepatotoxicity have been observed, such as ceramides with a sphingadienine backbone, octanoylcarnitine, creatine, acetylcholine, and ethoxylated phosphorylcholine. The combination of the metabolic fingerprint and footprint enabled a comprehensive investigation of the pathophysiology behind ethanol-induced hepatotoxicity.
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Affiliation(s)
- Elias Iturrospe
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.,Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | | | - Rani Robeyns
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | | | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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40
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Chávez-Márquez A, Gardea AA, González-Rios H, Vazquez-Moreno L. Characterization of Cabernet Sauvignon Wines by Untargeted HS-SPME GC-QTOF-MS. Molecules 2022; 27:1726. [PMID: 35268837 PMCID: PMC8911954 DOI: 10.3390/molecules27051726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
Untargeted metabolomics approaches are emerging as powerful tools for the quality evaluation and authenticity of food and beverages and have been applied to wine science. However, most fail to report the method validation, quality assurance and/or quality control applied, as well as the assessment through the metabolomics-methodology pipeline. Knowledge of Mexican viticulture, enology and wine science remains scarce, thus untargeted metabolomics approaches arise as a suitable tool. The aim of this study is to validate an untargeted HS-SPME-GC-qTOF/MS method, with attention to data processing to characterize Cabernet Sauvignon wines from two vineyards and two vintages. Validation parameters for targeted methods are applied in conjunction with the development of a recursive analysis of data. The combination of some parameters for targeted studies (repeatability and reproducibility < 20% RSD; linearity > 0.99; retention-time reproducibility < 0.5% RSD; match-identification factor < 2.0% RSD) with recursive analysis of data (101 entities detected) warrants that both chromatographic and spectrometry-processing data were under control and provided high-quality results, which in turn differentiate wine samples according to site and vintage. It also shows potential biomarkers that can be identified. This is a step forward in the pursuit of Mexican wine characterization that could be used as an authentication tool.
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Affiliation(s)
| | | | | | - Luz Vazquez-Moreno
- Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, CP., Hermosillo 83304, Sonora, Mexico; (A.C.-M.); (A.A.G.); (H.G.-R.)
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Järvilehto J, Harjuhaahto S, Palu E, Auranen M, Kvist J, Zetterberg H, Koskivuori J, Lehtonen M, Saukkonen AM, Jokela M, Ylikallio E, Tyynismaa H. Serum Creatine, Not Neurofilament Light, Is Elevated in CHCHD10-Linked Spinal Muscular Atrophy. Front Neurol 2022; 13:793937. [PMID: 35250809 PMCID: PMC8891230 DOI: 10.3389/fneur.2022.793937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Objective To characterize serum biomarkers in mitochondrial CHCHD10-linked spinal muscular atrophy Jokela (SMAJ) type for disease monitoring and for the understanding of pathogenic mechanisms. Methods We collected serum samples from a cohort of 49 patients with SMAJ, all carriers of the heterozygous c.197G>T p.G66V variant in CHCHD10. As controls, we used age- and sex-matched serum samples obtained from Helsinki Biobank. Creatine kinase and creatinine were measured by standard methods. Neurofilament light (NfL) and glial fibrillary acidic protein (GFAP) were measured with single molecule array (Simoa), fibroblast growth factor 21 (FGF-21), and growth differentiation factor 15 (GDF-15) with an enzyme-linked immunosorbent assay. For non-targeted plasma metabolite profiling, samples were analyzed with liquid chromatography high-resolution mass spectrometry. Disease severity was evaluated retrospectively by calculating a symptom-based score. Results Axon degeneration marker, NfL, was unexpectedly not altered in the serum of patients with SMAJ, whereas astrocytic activation marker, GFAP, was slightly decreased. Creatine kinase was elevated in most patients, particularly men. We identified six metabolites that were significantly altered in serum of patients with SMAJ in comparison to controls: increased creatine and pyruvate, and decreased creatinine, taurine, N-acetyl-carnosine, and succinate. Creatine correlated with disease severity. Altered pyruvate and succinate indicated a metabolic response to mitochondrial dysfunction; however, lactate or mitochondrial myopathy markers FGF-21 or GDF-15 was not changed. Conclusions Biomarkers of muscle mass and damage are altered in SMAJ serum, indicating a role for skeletal muscle in disease pathogenesis in addition to neurogenic damage. Despite the minimal mitochondrial pathology in skeletal muscle, signs of a metabolic shift can be detected.
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Affiliation(s)
- Julius Järvilehto
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sandra Harjuhaahto
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Edouard Palu
- Clinical Neurosciences, Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Mari Auranen
- Clinical Neurosciences, Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
- UK Dementia Research Institute at UCL, London, United Kingdom
| | | | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | | | - Manu Jokela
- Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
- Department of Neurology, Neuromuscular Research Center, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Clinical Neurosciences, Neurology, Helsinki University Hospital, Helsinki, Finland
- *Correspondence: Emil Ylikallio
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Henna Tyynismaa
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Pessa-Morikawa T, Husso A, Kärkkäinen O, Koistinen V, Hanhineva K, Iivanainen A, Niku M. Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta. BMC Microbiol 2022; 22:46. [PMID: 35130835 PMCID: PMC8819883 DOI: 10.1186/s12866-022-02457-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/29/2022] [Indexed: 12/20/2022] Open
Abstract
Background The maternal microbiota affects the development of the offspring by microbial metabolites translocating to the fetus. To reveal the spectrum of these molecular mediators of the earliest host-microbe interactions, we compared placenta, fetal intestine and brain from germ-free (GF) and specific pathogen free (SPF) mouse dams by non-targeted metabolic profiling. Results One hundred one annotated metabolites and altogether 3680 molecular features were present in significantly different amounts in the placenta and/or fetal organs of GF and SPF mice. More than half of these were more abundant in the SPF organs, suggesting their microbial origin or a metabolic response of the host to the presence of microbes. The clearest separation was observed in the placenta, but most of the molecular features showed significantly different levels also in the fetal intestine and/or brain. Metabolites that were detected in lower amounts in the GF fetal organs included 5-aminovaleric acid betaine, trimethylamine N-oxide, catechol-O-sulphate, hippuric and pipecolic acid. Derivatives of the amino acid tryptophan, such as kynurenine, 3-indolepropionic acid and hydroxyindoleacetic acid, were also less abundant in the absence of microbiota. Ninety-nine molecular features were detected only in the SPF mice. We also observed several molecular features which were more abundant in the GF mice, possibly representing precursors of microbial metabolites or indicators of a metabolic response to the absence of microbiota. Conclusions The maternal microbiota has a profound impact on the fetal metabolome. Our observations suggest the existence of a multitude of yet unidentified microbially modified metabolites which pass through the placenta into the fetus and potentially influence fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02457-6.
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Affiliation(s)
- Tiina Pessa-Morikawa
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Aleksi Husso
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland.,Afekta Technologies Ltd., Kuopio, Finland
| | - Ville Koistinen
- Afekta Technologies Ltd., Kuopio, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Food Chemistry and Food Development Unit, University of Turku, Turku, Finland
| | - Kati Hanhineva
- Afekta Technologies Ltd., Kuopio, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Food Chemistry and Food Development Unit, University of Turku, Turku, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Niku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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43
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Ronkainen J, Nedelec R, Atehortua A, Balkhiyarova Z, Cascarano A, Ngoc Dang V, Elhakeem A, van Enckevort E, Goncalves Soares A, Haakma S, Halonen M, Heil KF, Heiskala A, Hyde E, Jacquemin B, Keikkala E, Kerckhoffs J, Klåvus A, Kopinska JA, Lepeule J, Marazzi F, Motoc I, Näätänen M, Ribbenstedt A, Rundblad A, Savolainen O, Simonetti V, de Toro Eadie N, Tzala E, Ulrich A, Wright T, Zarei I, d’Amico E, Belotti F, Brunius C, Castleton C, Charles MA, Gaillard R, Hanhineva K, Hoek G, Holven KB, Jaddoe VWV, Kaakinen MA, Kajantie E, Kavousi M, Lakka T, Matthews J, Piano Mortari A, Vääräsmäki M, Voortman T, Webster C, Zins M, Atella V, Bulgheroni M, Chadeau-Hyam M, Conti G, Evans J, Felix JF, Heude B, Järvelin MR, Kolehmainen M, Landberg R, Lekadir K, Parusso S, Prokopenko I, de Rooij SR, Roseboom T, Swertz M, Timpson N, Ulven SM, Vermeulen R, Juola T, Sebert S. LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases. Environ Epidemiol 2022; 6:e184. [PMID: 35169663 PMCID: PMC8835657 DOI: 10.1097/ee9.0000000000000184] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 11/14/2021] [Indexed: 11/29/2022] Open
Abstract
The current epidemics of cardiovascular and metabolic noncommunicable diseases have emerged alongside dramatic modifications in lifestyle and living environments. These correspond to changes in our "modern" postwar societies globally characterized by rural-to-urban migration, modernization of agricultural practices, and transportation, climate change, and aging. Evidence suggests that these changes are related to each other, although the social and biological mechanisms as well as their interactions have yet to be uncovered. LongITools, as one of the 9 projects included in the European Human Exposome Network, will tackle this environmental health equation linking multidimensional environmental exposures to the occurrence of cardiovascular and metabolic noncommunicable diseases.
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Affiliation(s)
- Justiina Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Rozenn Nedelec
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Angelica Atehortua
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Zhanna Balkhiyarova
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Bashkir State Medical University, Department of Endocrinology, Ufa, Russian Federation
| | - Anna Cascarano
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Vien Ngoc Dang
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Ahmed Elhakeem
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Esther van Enckevort
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Ana Goncalves Soares
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Sido Haakma
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Miia Halonen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Katharina F. Heil
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Anni Heiskala
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Eleanor Hyde
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Bénédicte Jacquemin
- University of Rennes, INSERM, School of Advanced Studies in Public Health (EHESP), Research Institute for Environmental and Occupational Health, UMR_S 1085, Rennes, France
| | - Elina Keikkala
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jules Kerckhoffs
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Joanna A. Kopinska
- Department of Social Sciences and Economics, Sapienza University of Rome, Rome, Italy
| | - Johanna Lepeule
- Grenoble Alpes University, INSERM, CNRS, Institute for Advanced Biosciences, Grenoble, France
| | - Francesca Marazzi
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
| | - Irina Motoc
- Amsterdam UMC, Epidemiology and Data Science, University of Amsterdam, Amsterdam Public Health, Amsterdam, the Netherlands
| | - Mari Näätänen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Anton Ribbenstedt
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Amanda Rundblad
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Otto Savolainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Nina de Toro Eadie
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Evangelia Tzala
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Anna Ulrich
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Thomas Wright
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Iman Zarei
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | | | - Federico Belotti
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
- Department of Economics and Finance, University of Rome Tor Vergata, Rome, Italy
| | - Carl Brunius
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Marie-Aline Charles
- Center for Research in Epidemiology and Statistics, INSERM, INRAE, University of Paris, Paris, France
- Ined, INSERM, EFS, Elfe Joint Unit, Aubervilliers, France
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Gerard Hoek
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Kirsten B. Holven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
- National Advisory Unit on Familial Hypercholesterolemia, Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marika A. Kaakinen
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Timo Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Jason Matthews
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Andrea Piano Mortari
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
| | - Marja Vääräsmäki
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Marie Zins
- Population-based Epidemiological Cohorts Unit, INSERM UMS 11, Villejuif, France
| | - Vincenzo Atella
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
- Department of Economics and Finance, University of Rome Tor Vergata, Rome, Italy
- Stanford University, Stanford, CA
| | | | - Marc Chadeau-Hyam
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Gabriella Conti
- Department of Economics, University College London, London, United Kingdom
- Social Research Institute, London, United Kingdom
| | - Jayne Evans
- Beta Technology Ltd, Doncaster, United Kingdom
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Barbara Heude
- Center for Research in Epidemiology and Statistics, INSERM, INRAE, University of Paris, Paris, France
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Marjukka Kolehmainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karim Lekadir
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | | | - Inga Prokopenko
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- UMR 8199-EGID, Institut Pasteur de Lille, CNRS, University of Lille, Lille, France
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Susanne R. de Rooij
- Amsterdam UMC, Epidemiology and Data Science, University of Amsterdam, Amsterdam Public Health, Amsterdam, the Netherlands
| | - Tessa Roseboom
- Amsterdam UMC, Epidemiology and Data Science, University of Amsterdam, Amsterdam Public Health, Amsterdam, the Netherlands
- Gynaecology and Obstetrics, Amsterdam Reproduction and Development Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Morris Swertz
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Nicholas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Stine M. Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
- Julius Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Teija Juola
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Corresponding Author. Address: Faculty of Medicine, Center for Life Course Health Research, University of Oulu, PO Box 5000, FIN-90014, Finland. E-mail: (S. Sebert)
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Babu AF, Koistinen VM, Turunen S, Solano-Aguilar G, Urban JF, Zarei I, Hanhineva K. Identification and Distribution of Sterols, Bile Acids, and Acylcarnitines by LC-MS/MS in Humans, Mice, and Pigs-A Qualitative Analysis. Metabolites 2022; 12:metabo12010049. [PMID: 35050171 PMCID: PMC8781580 DOI: 10.3390/metabo12010049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 12/28/2022] Open
Abstract
Sterols, bile acids, and acylcarnitines are key players in human metabolism. Precise annotations of these metabolites with mass spectrometry analytics are challenging because of the presence of several isomers and stereoisomers, variability in ionization, and their relatively low concentrations in biological samples. Herein, we present a sensitive and simple qualitative LC–MS/MS (liquid chromatography with tandem mass spectrometry) method by utilizing a set of pure chemical standards to facilitate the identification and distribution of sterols, bile acids, and acylcarnitines in biological samples including human stool and plasma; mouse ileum, cecum, jejunum content, duodenum content, and liver; and pig bile, proximal colon, cecum, heart, stool, and liver. With this method, we detected 24 sterol, 32 bile acid, and 27 acylcarnitine standards in one analysis that were separated within 13 min by reversed-phase chromatography. Further, we observed different sterol, bile acid, and acylcarnitine profiles for the different biological samples across the different species. The simultaneous detection and annotation of sterols, bile acids, and acylcarnitines from reference standards and biological samples with high precision represents a valuable tool for screening these metabolites in routine scientific research.
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Affiliation(s)
- Ambrin Farizah Babu
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland; (V.M.K.); (I.Z.); (K.H.)
- Afekta Technologies Ltd., Yliopistonranta 1L, 70211 Kuopio, Finland;
- Correspondence: ; Tel.: +358-45-20-30-433
| | - Ville Mikael Koistinen
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland; (V.M.K.); (I.Z.); (K.H.)
- Afekta Technologies Ltd., Yliopistonranta 1L, 70211 Kuopio, Finland;
- Department of Biochemistry, Food Chemistry and Food Development Unit, University of Turku, 20014 Turku, Finland
| | - Soile Turunen
- Afekta Technologies Ltd., Yliopistonranta 1L, 70211 Kuopio, Finland;
- School of Pharmacy, University of Eastern Finland, 70210 Kuopio, Finland
| | - Gloria Solano-Aguilar
- U.S. Department of Agriculture, Agricultural Research Service, Northeast Area, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD 20705, USA; (G.S.-A.); (J.F.U.J.)
| | - Joseph F. Urban
- U.S. Department of Agriculture, Agricultural Research Service, Northeast Area, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD 20705, USA; (G.S.-A.); (J.F.U.J.)
| | - Iman Zarei
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland; (V.M.K.); (I.Z.); (K.H.)
| | - Kati Hanhineva
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland; (V.M.K.); (I.Z.); (K.H.)
- Afekta Technologies Ltd., Yliopistonranta 1L, 70211 Kuopio, Finland;
- Department of Biochemistry, Food Chemistry and Food Development Unit, University of Turku, 20014 Turku, Finland
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Leyrolle Q, Cserjesi R, Demeure R, Neyrinck AM, Amadieu C, Rodriguez J, Kärkkäinen O, Hanhineva K, Paquot N, Cnop M, Cani PD, Thissen JP, Bindels LB, Klein O, Luminet O, Delzenne NM. Microbiota and Metabolite Profiling as Markers of Mood Disorders: A Cross-Sectional Study in Obese Patients. Nutrients 2021; 14:nu14010147. [PMID: 35011021 PMCID: PMC8746987 DOI: 10.3390/nu14010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
Obesity is associated with an increased risk of several neurological and psychiatric diseases, but few studies report the contribution of biological features in the occurrence of mood disorders in obese patients. The aim of the study is to evaluate the potential links between serum metabolomics and gut microbiome, and mood disturbances in a cohort of obese patients. Psychological, biological characteristics and nutritional habits were evaluated in 94 obese subjects from the Food4Gut study stratified according to their mood score assessed by the Positive and Negative Affect Schedule (PANAS). The fecal gut microbiota and plasma non-targeted metabolomics were analysed. Obese subjects with increased negative mood display elevated levels of Coprococcus as well as decreased levels of Sutterella and Lactobacillus. Serum metabolite profile analysis reveals in these subjects altered levels of several amino acid-derived metabolites, such as an increased level of L-histidine and a decreased in phenylacetylglutamine, linked to altered gut microbiota composition and function rather than to differences in dietary amino acid intake. Regarding clinical profile, we did not observe any differences between both groups. Our results reveal new microbiota-derived metabolites that characterize the alterations of mood in obese subjects, thereby allowing to propose new targets to tackle mood disturbances in this context. Food4gut, clinicaltrial.gov: NCT03852069.
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Affiliation(s)
- Quentin Leyrolle
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
| | - Renata Cserjesi
- Center for Social and Cultural Psychology, Université Libre de Bruxelles, 1000 Brussels, Belgium; (R.C.); (O.K.)
- Institute of Psychology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Romane Demeure
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
| | - Audrey M. Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
| | - Camille Amadieu
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
| | - Julie Rodriguez
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
| | - Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland;
| | - Kati Hanhineva
- Food Chemistry and Food Development Unit, Department of Life Technologies, University of Turku, 20014 Turku, Finland;
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland
| | - Nicolas Paquot
- Laboratory of Immunometabolism and Nutrition, GIGA-Inflammation, Infection & Immunity, University of Liège, 4000 Liège, Belgium;
| | - Miriam Cnop
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium;
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Patrice D. Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
- WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, UCLouvain, 1200 Brussels, Belgium
| | - Jean-Paul Thissen
- Pole of Endocrinology, Diabetes and Nutrition, Institut de Recherche Expérimentale et Clinique IREC, UCLouvain, 1200 Brussels, Belgium;
| | - Laure B. Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
| | - Olivier Klein
- Center for Social and Cultural Psychology, Université Libre de Bruxelles, 1000 Brussels, Belgium; (R.C.); (O.K.)
| | - Olivier Luminet
- Research Institute for Psychological Sciences, UCLouvain, 1348 Louvain-la-Neuve, Belgium;
| | - Nathalie M. Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, 1200 Brussels, Belgium; (Q.L.); (R.D.); (A.M.N.); (C.A.); (J.R.); (P.D.C.); (L.B.B.)
- Correspondence: ; Tel.: +32-2-764-73-69
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Abraham EJ, Kellogg JJ. Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials. Front Nutr 2021; 8:780228. [PMID: 34901127 PMCID: PMC8663772 DOI: 10.3389/fnut.2021.780228] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/31/2021] [Indexed: 01/08/2023] Open
Abstract
Botanical supplements with broad traditional and medicinal uses represent an area of growing importance for American health management; 25% of U.S. adults use dietary supplements daily and collectively spent over $9. 5 billion in 2019 in herbal and botanical supplements alone. To understand how natural products benefit human health and determine potential safety concerns, careful in vitro, in vivo, and clinical studies are required. However, botanicals are innately complex systems, with complicated compositions that defy many standard analytical approaches and fluctuate based upon a plethora of factors, including genetics, growth conditions, and harvesting/processing procedures. Robust studies rely upon accurate identification of the plant material, and botanicals' increasing economic and health importance demand reproducible sourcing, as well as assessment of contamination or adulteration. These quality control needs for botanical products remain a significant problem plaguing researchers in academia as well as the supplement industry, thus posing a risk to consumers and possibly rendering clinical data irreproducible and/or irrelevant. Chemometric approaches that analyze the small molecule composition of materials provide a reliable and high-throughput avenue for botanical authentication. This review emphasizes the need for consistent material and provides insight into the roles of various modern chemometric analyses in evaluating and authenticating botanicals, focusing on advanced methodologies, including targeted and untargeted metabolite analysis, as well as the role of multivariate statistical modeling and machine learning in phytochemical characterization. Furthermore, we will discuss how chemometric approaches can be integrated with orthogonal techniques to provide a more robust approach to authentication, and provide directions for future research.
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Affiliation(s)
- Evelyn J Abraham
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University (PSU), University Park, PA, United States
| | - Joshua J Kellogg
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University (PSU), University Park, PA, United States.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
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Hughes SS, Nielsen MMK, Jonsbo RV, Nielsen CU, Lauritsen FR, Prabhala BK. BeerMIMS: Exploring the Use of Membrane-Inlet Mass Spectrometry (MIMS) Coupled to KNIME for the Characterization of Danish Beers. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2021; 27:266-271. [PMID: 34989272 DOI: 10.1177/14690667211073317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Beer is a complex mix of more than 7700 compounds, around 800 of which are volatile. While GC-MS has been actively employed in the analysis of the volatome of beer, this method is challenged by the complex nature of the sample. Herein, we explored the possible of using membrane-inlet mass spectrometry (MIMS) coupled to KNIME to characterize local Danish beers. KNIME stands for Konstanz Information Miner and is a free open-source data processing software which comes with several prebuilt nodes, that, when organized, result in data processing workflows allowing swift analysis of data with outputs that can be visualized in the desired format. KNIME has been shown to be promising in automation of large datasets and requires very little computing power. In fact, most of the computations can be carried out on a regular PC. Herein, we have utilized a KNIME workflow for data visualization of MIMS data to understand the global volatome of beers. Feature identification was not possible as of now but with a combination of MIMS and a KNIME workflow, we were able to distinguish beers from different micro-breweries located in Denmark, laying the foundation for the use of MIMS in future analysis of the beer volatome.
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Affiliation(s)
| | - Marcus M K Nielsen
- Department of Physics, Chemistry and Pharmacy, 6174University of Southern Denmark, 5230 Odense M, Denmark
| | - Rasmus Voersaa Jonsbo
- Department of Physics, Chemistry and Pharmacy, 6174University of Southern Denmark, 5230 Odense M, Denmark
| | - Carsten Uhd Nielsen
- Department of Physics, Chemistry and Pharmacy, 6174University of Southern Denmark, 5230 Odense M, Denmark
| | - Frants Roager Lauritsen
- Department of Physics, Chemistry and Pharmacy, 6174University of Southern Denmark, 5230 Odense M, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry and Pharmacy, 6174University of Southern Denmark, 5230 Odense M, Denmark
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Kärkkäinen O, Kokla M, Lehtonen M, Auriola S, Martiskainen M, Tiihonen J, Karhunen PJ, Hanhineva K, Kok E. Changes in the metabolic profile of human male postmortem frontal cortex and cerebrospinal fluid samples associated with heavy alcohol use. Addict Biol 2021; 26:e13035. [PMID: 33745230 DOI: 10.1111/adb.13035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022]
Abstract
Heavy alcohol use is one of the top causes of disease and death in the world. The brain is a key organ affected by heavy alcohol use. Here, our aim was to measure changes caused by heavy alcohol use in the human brain metabolic profile. We analyzed human postmortem frontal cortex and cerebrospinal fluid (CSF) samples from males with a history of heavy alcohol use (n = 74) and controls (n = 74) of the Tampere Sudden Death Series cohort. We used a nontargeted liquid chromatography mass spectrometry-based metabolomics method. We observed differences between the study groups in the metabolite levels of both frontal cortex and CSF samples, for example, in amino acids and derivatives, and acylcarnitines. There were more significant alterations in the metabolites of frontal cortex than in CSF. In the frontal cortex, significant alterations were seen in the levels of neurotransmitters (e.g., decreased levels of GABA and acetylcholine), acylcarnitines (e.g., increased levels of acylcarnitine 4:0), and in some metabolites associated with alcohol metabolizing enzymes (e.g., increased levels of 2-piperidone). Some of these changes were also significant in the CSF samples (e.g., elevated 2-piperidone levels). Overall, these results show the metabolites associated with neurotransmitters, energy metabolism and alcohol metabolism, were altered in human postmortem frontal cortex and CSF samples of persons with a history of heavy alcohol use.
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Affiliation(s)
- Olli Kärkkäinen
- School of Pharmacy University of Eastern Finland Kuopio Finland
| | - Marietta Kokla
- Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio Finland
| | - Marko Lehtonen
- School of Pharmacy University of Eastern Finland Kuopio Finland
| | - Seppo Auriola
- School of Pharmacy University of Eastern Finland Kuopio Finland
| | - Mika Martiskainen
- Faculty of Medicine and Health Technology Tampere University and Fimlab Laboratories Ltd, Tampere University Hospital Region Kuopio Finland
- Finnish Institute for Health and Welfare Finland
| | - Jari Tiihonen
- Department of Forensic Psychiatry University of Eastern Finland, Niuvanniemi Hospital Helsinki Finland
- Department of Clinical Neuroscience Karolinska Institutet and Center for Psychiatry Research, Stockholm City Council Stockholm Sweden
| | - Pekka J. Karhunen
- Faculty of Medicine and Health Technology Tampere University and Fimlab Laboratories Ltd, Tampere University Hospital Region Kuopio Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio Finland
- Department of Biochemistry, Food chemistry and food development unit University of Turku Turku Finland
| | - Eloise Kok
- Faculty of Medicine and Health Technology Tampere University and Fimlab Laboratories Ltd, Tampere University Hospital Region Kuopio Finland
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Kärkkäinen O, Farokhnia M, Klåvus A, Auriola S, Lehtonen M, Deschaine SL, Piacentino D, Abshire KM, Jackson SN, Leggio L. Effect of intravenous ghrelin administration, combined with alcohol, on circulating metabolome in heavy drinking individuals with alcohol use disorder. Alcohol Clin Exp Res 2021; 45:2207-2216. [PMID: 34590334 PMCID: PMC8642277 DOI: 10.1111/acer.14719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Ghrelin may influence several alcohol-related behaviors in animals and humans by modulating central and/or peripheral biological pathways. The aim of this exploratory analysis was to investigate associations between ghrelin administration and the human circulating metabolome during alcohol exposure in nontreatment seeking, heavy drinking individuals with alcohol use disorder (AUD). METHODS We used serum samples from a randomized, crossover, double-blind, placebo-controlled human laboratory study with intravenous (IV) ghrelin or placebo infusion in two experiments. During each session, participants received a loading dose (3 µg/kg) followed by continuous infusion (16.9 ng/kg/min) of acyl ghrelin or placebo. The first experiment included an IV alcohol self-administration (IV-ASA) session and the second experiment included an IV alcohol clamp (IV-AC) session, both with the counterbalanced infusion of ghrelin or placebo. Serum metabolite profiles were analyzed from repeated blood samples collected during each session. RESULTS In both experiments, ghrelin infusion was associated with an altered serum metabolite profile, including significantly increased levels of cortisol (IV-ASA q-value = 0.0003 and IV-AC q < 0.0001), corticosterone (IV-ASA q = 0.0202 and IV-AC q < 0.0001), and glycochenodeoxycholic acid (IV-ASA q = 0.0375 and IV-AC q = 0.0013). In the IV-ASA experiment, ghrelin infusion increased levels of cortisone (q = 0.0352) and fatty acids 18:1 (q = 0.0406) and 18:3 (q = 0.0320). Moreover, in the IV-AC experiment, ghrelin infusion significantly increased levels of glycocholic acid (q < 0.0001) and phenylalanine (q = 0.0458). CONCLUSION IV ghrelin infusion, combined with IV alcohol administration, was associated with increases in the circulating metabolite levels of corticosteroids and glycine-conjugated bile acids, among other changes. Further research is needed to understand the role that metabolomic changes play in the complex interaction between ghrelin and alcohol.
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Affiliation(s)
- Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Mehdi Farokhnia
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, Baltimore and Bethesda, Maryland, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Sara L. Deschaine
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, Baltimore and Bethesda, Maryland, USA
| | - Daria Piacentino
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, Baltimore and Bethesda, Maryland, USA
- Center on Compulsive Behaviors, National Institutes of Health, Bethesda, MD, USA
| | - Kelly M. Abshire
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, Baltimore and Bethesda, Maryland, USA
| | - Shelley N. Jackson
- Translational Analytical Core, National Institute on Drug Abuse Intramural Research Program, Baltimore, Maryland, USA
| | - Lorenzo Leggio
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, Baltimore and Bethesda, Maryland, USA
- Center on Compulsive Behaviors, National Institutes of Health, Bethesda, MD, USA
- Translational Analytical Core, National Institute on Drug Abuse Intramural Research Program, Baltimore, Maryland, USA
- Medication Development Program, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
- Center for Alcohol and Addiction Studies, Department of Behavioral and Social Sciences, Brown University, Providence, RI, USA
- Division of Addiction Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, USA
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The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. Metabolites 2021; 11:metabo11110713. [PMID: 34822371 PMCID: PMC8624948 DOI: 10.3390/metabo11110713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022] Open
Abstract
Lipidomics is a newly emerged discipline involving the identification and quantification of thousands of lipids. As a part of the omics field, lipidomics has shown rapid growth both in the number of studies and in the size of lipidome datasets, thus, requiring specific and efficient data analysis approaches. This paper aims to provide guidelines for analyzing and interpreting lipidome data obtained using untargeted methods that rely on liquid chromatography coupled with mass spectrometry (LC-MS) to detect and measure the intensities of lipid compounds. We present a state-of-the-art untargeted LC-MS workflow for lipidomics, from study design to annotation of lipid features, focusing on practical, rather than theoretical, approaches for data analysis, and we outline possible applications of untargeted lipidomics for biological studies. We provide a detailed R notebook designed specifically for untargeted lipidome LC-MS data analysis, which is based on xcms software.
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