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Day F, O'Sullivan J, Ramzan F, Pook C. Polar metabolomics using trichloroacetic acid extraction and porous graphitic carbon stationary phase. Metabolomics 2024; 20:77. [PMID: 39014104 PMCID: PMC11252196 DOI: 10.1007/s11306-024-02146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
INTRODUCTION Accurately identifying and quantifying polar metabolites using untargeted metabolomics has proven challenging in comparison to mid to non-polar metabolites. Hydrophilic interaction chromatography and gas chromatography-mass spectrometry are predominantly used to target polar metabolites. OBJECTIVES This study aims to demonstrate a simple one-step extraction combined with liquid chromatography-mass spectrometry (LC-MS) that reliably retains polar metabolites. METHODS The method involves a MilliQ + 10% trichloroacetic acid extraction from 6 healthy individuals serum, combined with porous graphitic carbon liquid chromatography-mass spectrometry (LC-MS). The coefficient of variation (CV) assessed retention reliability of polar metabolites with logP as low as - 9. QreSS (Quantification, Retention, and System Suitability) internal standards determined the method's consistency and recovery efficiency. RESULTS The method demonstrated reliable retention (CV < 0.30) of polar metabolites within a logP range of - 9.1 to 5.6. QreSS internal standards confirmed consistent performance (CV < 0.16) and effective recovery (70-130%) of polar to mid-polar metabolites. Quality control dilution series demonstrated that ~ 80% of annotated metabolites could be accurately quantified (Pearson's correlation coefficient > 0.80) within their concentration range. Repeatability was demonstrated through clustering of repeated extractions from a single sample. CONCLUSION This LC-MS method is better suited to covering the polar segment of the metabolome than current methods, offering a reliable and efficient approach for accurate quantification of polar metabolites in untargeted metabolomics.
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Affiliation(s)
- Francesca Day
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Justin O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Australian Parkinson's Mission, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, Darlinghurst, NSW, 2010, Australia
- A*STAR Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Farha Ramzan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Chris Pook
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- School of Chemical Sciences, University of Auckland, 23 Symonds St., Auckland, 1010, New Zealand.
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2
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Gelambi M, Whitehead SR. Untargeted Metabolomics Reveals Fruit Secondary Metabolites Alter Bat Nutrient Absorption. J Chem Ecol 2024:10.1007/s10886-024-01503-z. [PMID: 38758510 DOI: 10.1007/s10886-024-01503-z] [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] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The ecological interaction between fleshy fruits and frugivores is influenced by diverse mixtures of secondary metabolites that naturally occur in the fruit pulp. Although some fruit secondary metabolites have a primary role in defending the pulp against antagonistic frugivores, these metabolites also potentially affect mutualistic interactions. The physiological impact of these secondary metabolites on mutualistic frugivores remains largely unexplored. Using a mutualistic fruit bat (Carollia perspicillata), we showed that ingesting four secondary metabolites commonly found in plant tissues affects bat foraging behavior and induces changes in the fecal metabolome. Our behavioral trials showed that the metabolites tested typically deter bats. Our metabolomic surveys suggest that secondary metabolites alter, either by increasing or decreasing, the absorption of essential macronutrients. These behavioral and physiological effects vary based on the specific identity and concentration of the metabolite tested. Our results also suggest that a portion of the secondary metabolites consumed is excreted by the bat intact or slightly modified. By identifying key shifts in the fecal metabolome of a mutualistic frugivore caused by secondary metabolite consumption, this study improves our understanding of the effects of fruit chemistry on frugivore physiology.
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Affiliation(s)
- Mariana Gelambi
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Latham Hall RM 427, 220 Ag Quad Lane, Blacksburg, VA, 24060, USA.
- La Selva Biological Station, Organization for Tropical Studies, Puerto Viejo de Sarapiquí, Heredia Province, Costa Rica.
| | - Susan R Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Latham Hall RM 427, 220 Ag Quad Lane, Blacksburg, VA, 24060, USA
- La Selva Biological Station, Organization for Tropical Studies, Puerto Viejo de Sarapiquí, Heredia Province, Costa Rica
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3
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Collado-Perez R, Chamoso-Sánchez D, García A, Fernández-Alfonso MS, Jiménez-Hernáiz M, Canelles S, Argente J, Frago LM, Chowen JA. The differential effects of palmitic acid and oleic acid on the metabolic response of hypothalamic astrocytes from male and female mice. J Neurosci Res 2024; 102:e25339. [PMID: 38741550 DOI: 10.1002/jnr.25339] [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: 11/28/2023] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024]
Abstract
Diets rich in saturated fats are more detrimental to health than those containing mono- or unsaturated fats. Fatty acids are an important source of energy, but they also relay information regarding nutritional status to hypothalamic metabolic circuits and when in excess can be detrimental to these circuits. Astrocytes are the main site of central fatty acid β-oxidation, and hypothalamic astrocytes participate in energy homeostasis, in part by modulating hormonal and nutritional signals reaching metabolic neurons, as well as in the inflammatory response to high-fat diets. Thus, we hypothesized that how hypothalamic astrocytes process-specific fatty acids participates in determining the differential metabolic response and that this is sex dependent as males and females respond differently to high-fat diets. Male and female primary hypothalamic astrocyte cultures were treated with oleic acid (OA) or palmitic acid (PA) for 24 h, and an untargeted metabolomics study was performed. A clear predictive model for PA exposure was obtained, while the metabolome after OA exposure was not different from controls. The observed modifications in metabolites, as well as the expression levels of key metabolic enzymes, indicate a reduction in the activity of the Krebs and glutamate/glutamine cycles in response to PA. In addition, there were specific differences between the response of astrocytes from male and female mice, as well as between hypothalamic and cerebral cortical astrocytes. Thus, the response of hypothalamic astrocytes to specific fatty acids could result in differential impacts on surrounding metabolic neurons and resulting in varied systemic metabolic outcomes.
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Affiliation(s)
- Roberto Collado-Perez
- Department of Endocrinology, Instituto de Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - David Chamoso-Sánchez
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Antonia García
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | | | - Maria Jiménez-Hernáiz
- Department of Endocrinology, Instituto de Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Sandra Canelles
- Department of Endocrinology, Instituto de Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Argente
- Department of Endocrinology, Instituto de Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Laura M Frago
- Department of Endocrinology, Instituto de Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie A Chowen
- Department of Endocrinology, Instituto de Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain
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4
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Fall F, Desmet L, Mamede L, Schioppa L, de Tullio P, Frédérich M, Govaerts B, Quetin-Leclercq J. Comparison of Three Widely Employed Extraction Methods for Metabolomic Analysis of Trypanosoma brucei. Curr Protoc 2024; 4:e1043. [PMID: 38706422 DOI: 10.1002/cpz1.1043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Trypanosoma brucei (Tb) is the causative agent of human African trypanosomiasis (HAT), also known as sleeping sickness, which can be fatal if left untreated. An understanding of the parasite's cellular metabolism is vital for the discovery of new antitrypanosomal drugs and for disease eradication. Metabolomics can be used to analyze numerous metabolic pathways described as essential to Tb. brucei but has some limitations linked to the metabolites' physicochemical properties and the extraction process. To develop an optimized method for extracting and analyzing Tb. brucei metabolites, we tested the three most commonly used extraction methods, analyzed the extracts by hydrophilic interaction liquid chromatography high-resolution mass spectrometry (HILIC LC-HRMS), and further evaluated the results using quantitative criteria including the number, intensity, reproducibility, and variability of features, as well as qualitative criteria such as the specific coverage of relevant metabolites. Here, we present the resulting protocols for untargeted metabolomic analysis of Tb. brucei using (HILIC LC-HRMS). © 2024 Wiley Periodicals LLC. Basic Protocol 1: Culture of Trypanosoma brucei brucei parasites Basic Protocol 2: Preparation of samples for metabolomic analysis of Trypanosoma brucei brucei Basic Protocol 3: LC-HRMS-based metabolomic data analysis of Trypanosoma brucei brucei.
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Affiliation(s)
- Fanta Fall
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Lieven Desmet
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA/LIDAM), UCLouvain, Louvain-la-Neuve, Belgium
| | - Lúcia Mamede
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Laura Schioppa
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Pascal de Tullio
- Metabolomics group, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Bernadette Govaerts
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA/LIDAM), UCLouvain, Louvain-la-Neuve, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
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Rojo-Sánchez A, Carmona-Martes A, Díaz-Olmos Y, Santamaría-Torres M, Cala MP, Orozco-Acosta E, Aroca-Martínez G, Pacheco-Londoño L, Navarro-Quiroz E, Pacheco-Lugo LA. Urinary metabolomic profiling of a cohort of Colombian patients with systemic lupus erythematosus. Sci Rep 2024; 14:9555. [PMID: 38664528 PMCID: PMC11045835 DOI: 10.1038/s41598-024-60217-0] [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: 12/22/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune and multisystem disease with a high public health impact. Lupus nephritis (LN), commonly known as renal involvement in SLE, is associated with a poorer prognosis and increased rates of morbidity and mortality in patients with SLE. Identifying new urinary biomarkers that can be used for LN prognosis or diagnosis is essential and is part of current active research. In this study, we applied an untargeted metabolomics approach involving liquid and gas chromatography coupled with mass spectrometry to urine samples collected from 17 individuals with SLE and no kidney damage, 23 individuals with LN, and 10 clinically healthy controls (HCs) to identify differential metabolic profiles for SLE and LN. The data analysis revealed a differentially abundant metabolite expression profile for each study group, and those metabolites may act as potential differential biomarkers of SLE and LN. The differential metabolic pathways found between the LN and SLE patients with no kidney involvement included primary bile acid biosynthesis, branched-chain amino acid synthesis and degradation, pantothenate and coenzyme A biosynthesis, lysine degradation, and tryptophan metabolism. Receiver operating characteristic curve analysis revealed that monopalmitin, glycolic acid, and glutamic acid allowed for the differentiation of individuals with SLE and no kidney involvement and individuals with LN considering high confidence levels. While the results offer promise, it is important to recognize the significant influence of medications and other external factors on metabolomics studies. This impact has the potential to obscure differences in metabolic profiles, presenting a considerable challenge in the identification of disease biomarkers. Therefore, experimental validation should be conducted with a larger sample size to explore the diagnostic potential of the metabolites found as well as to examine how treatment and disease activity influence the identified chemical compounds. This will be crucial for refining the accuracy and effectiveness of using urine metabolomics for diagnosing and monitoring lupus and lupus nephritis.
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Affiliation(s)
- Alejandra Rojo-Sánchez
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia
| | - Ada Carmona-Martes
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia
| | - Yirys Díaz-Olmos
- Health Sciences Division, Medicine Program, Universidad del Norte, Barranquilla, Colombia
| | - Mary Santamaría-Torres
- Metabolomics Core Facility-MetCore, Vice-Presidency for Research, Universidad de los Andes, Bogotá, Colombia
| | - Mónica P Cala
- Metabolomics Core Facility-MetCore, Vice-Presidency for Research, Universidad de los Andes, Bogotá, Colombia
| | - Erick Orozco-Acosta
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia
| | - Gustavo Aroca-Martínez
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia
- Clínica de la Costa, Barranquilla, Colombia
| | - Leonardo Pacheco-Londoño
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia
| | - Elkin Navarro-Quiroz
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia
| | - Lisandro A Pacheco-Lugo
- Life Sciences Research Center, School of Basic and Biomedical Sciences, Universidad Simón Bolívar, Barranquilla, Colombia.
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Zhang Y, Pan Y, Bai X, Sun W, Zhou X, Dong Q, Wang H, Zhang Y, Bai W, Zhang W. Deciphering the impact of greenhouse pesticides on hepatic metabolism profile: Toxicity experiments on HepG2 cells using chlorpyrifos and emamectin benzoate. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 275:116230. [PMID: 38552389 DOI: 10.1016/j.ecoenv.2024.116230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/28/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024]
Abstract
Epidemiological evidence on the health effects of pesticide exposure among greenhouse workers is limited, and the mechanisms are lacking. Building upon our team's previous population study, we selected two pesticides, CPF and EB, with high detection rates, based on the theoretical foundation that the liver serves as a detoxifying organ, we constructed a toxicity model using HepG2 cells to investigate the impact of individual or combined pesticide exposure on the hepatic metabolism profile, attempting to identify targeted biomarkers. Our results showed that CPF and EB could significantly affect the survival rate of HepG2 cells and disrupt their metabolic profile. There were 117 metabolites interfered by CPF exposure, which mainly affected ABC transporter, biosynthesis of amino acids, center carbon metabolism in cancer, fatty acid biosynthesis and other pathways, 95 metabolites interfered by EB exposure, which mainly affected center carbon metabolism in cancer, HIF-1 signaling pathway, valine, leucine and isoleucine biosynthesis, fatty acid biosynthesis and other pathways. The cross analysis and further biological experiments confirmed that CPF and EB pesticide exposure may affect the HIF-1 signaling pathway and valine, leucine and isoleucine biosynthesis in HepG2 cells, providing reliable experimental evidence for the prevention and treatment of liver damage in greenhouse workers.
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Affiliation(s)
- Yingying Zhang
- Shanxi Key Laboratory of Environmental Health Impairment and Prevention, NHC Key Laboratory of Pneumoconiosis, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, China
| | - Yun Pan
- Shanxi Key Laboratory of Environmental Health Impairment and Prevention, NHC Key Laboratory of Pneumoconiosis, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, China
| | - Xiangyu Bai
- Shanxi Key Laboratory of Environmental Health Impairment and Prevention, NHC Key Laboratory of Pneumoconiosis, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, China
| | - Wen Sun
- Shanxi Key Laboratory of Environmental Health Impairment and Prevention, NHC Key Laboratory of Pneumoconiosis, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, China
| | - Xingfan Zhou
- Training Academy for Executive Leadership, Ministry of Emergency Mangement, Beijing 100054, China
| | - Qing Dong
- Changzhi maternal and child health care hospital, Shanxi 030001, China
| | - Hui Wang
- Changzhi maternal and child health care hospital, Shanxi 030001, China
| | - Yuanbao Zhang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China
| | - Wenlin Bai
- Shanxi Key Laboratory of Environmental Health Impairment and Prevention, NHC Key Laboratory of Pneumoconiosis, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, China
| | - Wenping Zhang
- Shanxi Key Laboratory of Environmental Health Impairment and Prevention, NHC Key Laboratory of Pneumoconiosis, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, China.
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7
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Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M, Villaseñor A. Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach. Nat Commun 2024; 15:3004. [PMID: 38589361 PMCID: PMC11001937 DOI: 10.1038/s41467-024-47182-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.
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Affiliation(s)
- Tomás Clive Barker-Tejeda
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Elisa Zubeldia-Varela
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Andrea Macías-Camero
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Lola Alonso
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Isabel Adoración Martín-Antoniano
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Instituto de Estudios de las Adicciones IEA-CEU, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - María Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Leticia Mera-Berriatua
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Raphaëlle Bazire
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Paula Cabrera-Freitag
- Pedriatic Allergy Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, and Gregorio Marañón Health Research Institute, Madrid, Spain
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Carles Ubeda
- Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - M Pilar Francino
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO) and Institut de Biologia Integrativa de Sistemes (Universitat de València / Consejo Superior de Investigaciones Científicas), València, Spain
| | - Domingo Barber
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - María Dolores Ibáñez-Sandín
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Marina Pérez-Gordo
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
| | - Alma Villaseñor
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
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8
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Bajo-Fernández M, Montero G, Alonso-Herranz V, Barbas C, Rey-Stolle F, García A. Structural elucidation of derivatives of polyfunctional metabolites after methyl chloroformate derivatization by high-resolution mass spectrometry gas chromatography. Application to microbiota metabolites. J Chromatogr A 2024; 1717:464656. [PMID: 38301332 DOI: 10.1016/j.chroma.2024.464656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Metabolomics has become an essential discipline in the study of microbiome, emerging gas chromatography coupled to mass spectrometry as the most mature, robust, and reproducible analytical technique. Silylation is the most widely used chemical derivatization strategy, although it has some limitations. In this regard, alkylation by alkyl chloroformate offers some advantages, such as a rapid reaction, milder conditions, better reproducibility, and the generation of more stable derivatives. However, commercial spectral libraries do not include many of the alkyl derivatives, mainly for polyfunctional metabolites, which can form multiple derivatives. That introduces a huge bias in untargeted metabolomics leading to common errors such as duplicates, unknowns, misidentifications, wrong assignations, and incomplete results from which non-reliable findings and conclusions will be retrieved. For this reason, the purpose of this study is to overcome these shortcomings and to expand the knowledge of metabolites in general and especially those closely related to the gut microbiota through the thorough study of the reactivity of the different functional groups in real matrix derivatized by methyl chloroformate, a common representative alkylation reagent. To this end, a systematic workflow has been developed based on exhaustive structural elucidation, along with computational simulation, and taking advantage of the high sensitivity and high-resolution gas chromatography-mass spectrometry. Several empirical rules have been established according to chemically different entities (free fatty acids, amino acids, polyols, sugars, amines, and polyfunctional groups, etc.) to predict the number of derivatives formed from a single metabolite, as well as their elution order and structure. In this work, some methyl chloroformate derivatives not previously reported as well as the mechanisms to explain them are given. Extremely important is the interconversion of E- and Z- geometric isomers of unsaturated dicarboxylic acids (case of fumaric-maleic and case of citraconic-mesaconic acids), or the formation of cycled derivatives for amino acids, as well as common metabolites, as in the case of serine and cysteine, and many others.
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Affiliation(s)
- M Bajo-Fernández
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - G Montero
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - V Alonso-Herranz
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - C Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - F Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - A García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain.
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9
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Bajo-Fernández M, Souza-Silva ÉA, Barbas C, Rey-Stolle MF, García A. GC-MS-based metabolomics of volatile organic compounds in exhaled breath: applications in health and disease. A review. Front Mol Biosci 2024; 10:1295955. [PMID: 38298553 PMCID: PMC10828970 DOI: 10.3389/fmolb.2023.1295955] [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: 09/17/2023] [Accepted: 12/05/2023] [Indexed: 02/02/2024] Open
Abstract
Exhaled breath analysis, with particular emphasis on volatile organic compounds, represents a growing area of clinical research due to its obvious advantages over other diagnostic tests. Numerous pathologies have been extensively investigated for the identification of specific biomarkers in exhalates through metabolomics. However, the transference of breath tests to clinics remains limited, mainly due to deficiency in methodological standardization. Critical steps include the selection of breath sample types, collection devices, and enrichment techniques. GC-MS is the reference analytical technique for the analysis of volatile organic compounds in exhalates, especially during the biomarker discovery phase in metabolomics. This review comprehensively examines and compares metabolomic studies focusing on cancer, lung diseases, and infectious diseases. In addition to delving into the experimental designs reported, it also provides a critical discussion of the methodological aspects, ranging from the experimental design and sample collection to the identification of potential pathology-specific biomarkers.
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Affiliation(s)
- María Bajo-Fernández
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Érica A. Souza-Silva
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Departmento de Química, Universidade Federal de São Paulo (UNIFESP), Diadema, Brazil
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Ma Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Antonia García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
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10
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Arias-Borrego A, Callejón-Leblic B, Collado MC, Abril N, García-Barrera T. Omics insights into the responses to dietary selenium. Proteomics 2023; 23:e2300052. [PMID: 37821362 DOI: 10.1002/pmic.202300052] [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: 06/21/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Selenium is a well-known health-relevant element related with cancer chemoprevention, neuroprotective roles, beneficial in diabetes, and in several infectious diseases, among others. It is naturally present in some foods, but deficiency in people led to the production of nutraceuticals, supplements, and functional food enriched in this element. There is a U-shaped link between selenium levels and health and a narrow range between toxic and essential levels, and thus, supplementation should be performed carefully. Omics methodologies have become valuable approaches to delve into the responses of dietary selenium in mammals that allowed a deeper knowledge about the metabolism of this element as well as its biological role. In this review, we discuss omics approaches from the workflows to their applications that has been previously used to deep insight into the metabolism of dietary selenium. There is a special focus on selenoproteins, metabolomics responses in blood and tissues (e.g., brain, reproductive organs, etc.) as well as the impact on gut microbiota and its metabolites profile. Thus, we mainly reviewed heteroatom-tagged proteomics, metallomics, metabolomics, and metataxonomics, usually combined with transcriptomics, genomics, and other molecular methods.
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Grants
- UHU-202009 Spanish Ministry of Economy and Competitiveness (MINECO)
- PY20_00366 Spanish Ministry of Economy and Competitiveness (MINECO)
- FEDER Andalusian Operative Program 2014-2020 (Ministry of Economy, Knowledge, Business and Universities, Regional Government of Andalusia, Spain)
- UNHU13-1E-1611 FEDER (European Community)
- PID2021-123073NB-C21 Ministerio de Ciencia e Innovación
- PY20_00366 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía
- UHU-202009 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía
- CEX2021-001189-S/MCIN/AEI/10.13039/501100011033 Spanish Government MCIN/AE-Center of Excellence Accreditation Severo Ochoa
- PID2022-139475OB-I00 Spanish Ministry of Science and Innovation (MCIN)
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Affiliation(s)
- Ana Arias-Borrego
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
- Department of Analytical Chemistry, Faculty of Chemistry, University of Sevilla, Profesor García González Ave., Seville, Spain
| | - Belén Callejón-Leblic
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, Spain
| | - Tamara García-Barrera
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
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11
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Fernández-García M, Ares-Arroyo M, Wedel E, Montero N, Barbas C, Rey-Stolle MF, González-Zorn B, García A. Multiplatform Metabolomics Characterization Reveals Novel Metabolites and Phospholipid Compositional Rules of Haemophilus influenzae Rd KW20. Int J Mol Sci 2023; 24:11150. [PMID: 37446331 DOI: 10.3390/ijms241311150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Haemophilus influenzae is a gram-negative bacterium of relevant clinical interest. H. influenzae Rd KW20 was the first organism to be sequenced and for which a genome-scale metabolic model (GEM) was developed. However, current H. influenzae GEMs are unable to capture several aspects of metabolome nature related to metabolite pools. To directly and comprehensively characterize the endometabolome of H. influenzae Rd KW20, we performed a multiplatform MS-based metabolomics approach combining LC-MS, GC-MS and CE-MS. We obtained direct evidence of 15-20% of the endometabolome present in current H. influenzae GEMs and showed that polar metabolite pools are interconnected through correlating metabolite islands. Notably, we obtained high-quality evidence of 18 metabolites not previously included in H. influenzae GEMs, including the antimicrobial metabolite cyclo(Leu-Pro). Additionally, we comprehensively characterized and evaluated the quantitative composition of the phospholipidome of H. influenzae, revealing that the fatty acyl chain composition is largely independent of the lipid class, as well as that the probability distribution of phospholipids is mostly related to the conditional probability distribution of individual acyl chains. This finding enabled us to provide a rationale for the observed phospholipid profiles and estimate the abundance of low-level species, permitting the expansion of the phospholipidome characterization through predictive probabilistic modelling.
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Affiliation(s)
- Miguel Fernández-García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Emilia Wedel
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| | - Mª Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
| | - Bruno González-Zorn
- Antimicrobial Resistance Unit (ARU), Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Complutense University of Madrid, 28040 Madrid, Spain
| | - Antonia García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
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12
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Paredes A, Justo-Méndez R, Jiménez-Blasco D, Núñez V, Calero I, Villalba-Orero M, Alegre-Martí A, Fischer T, Gradillas A, Sant'Anna VAR, Were F, Huang Z, Hernansanz-Agustín P, Contreras C, Martínez F, Camafeita E, Vázquez J, Ruiz-Cabello J, Area-Gómez E, Sánchez-Cabo F, Treuter E, Bolaños JP, Estébanez-Perpiñá E, Rupérez FJ, Barbas C, Enríquez JA, Ricote M. γ-Linolenic acid in maternal milk drives cardiac metabolic maturation. Nature 2023; 618:365-373. [PMID: 37225978 DOI: 10.1038/s41586-023-06068-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/11/2023] [Indexed: 05/26/2023]
Abstract
Birth presents a metabolic challenge to cardiomyocytes as they reshape fuel preference from glucose to fatty acids for postnatal energy production1,2. This adaptation is triggered in part by post-partum environmental changes3, but the molecules orchestrating cardiomyocyte maturation remain unknown. Here we show that this transition is coordinated by maternally supplied γ-linolenic acid (GLA), an 18:3 omega-6 fatty acid enriched in the maternal milk. GLA binds and activates retinoid X receptors4 (RXRs), ligand-regulated transcription factors that are expressed in cardiomyocytes from embryonic stages. Multifaceted genome-wide analysis revealed that the lack of RXR in embryonic cardiomyocytes caused an aberrant chromatin landscape that prevented the induction of an RXR-dependent gene expression signature controlling mitochondrial fatty acid homeostasis. The ensuing defective metabolic transition featured blunted mitochondrial lipid-derived energy production and enhanced glucose consumption, leading to perinatal cardiac dysfunction and death. Finally, GLA supplementation induced RXR-dependent expression of the mitochondrial fatty acid homeostasis signature in cardiomyocytes, both in vitro and in vivo. Thus, our study identifies the GLA-RXR axis as a key transcriptional regulatory mechanism underlying the maternal control of perinatal cardiac metabolism.
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Affiliation(s)
- Ana Paredes
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Raquel Justo-Méndez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Daniel Jiménez-Blasco
- Institute of Functional Biology and Genomics (IBFG), University of Salamanca, CSIC, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Vanessa Núñez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Irene Calero
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - María Villalba-Orero
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Departamento de Medicina y Cirugía Animal, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Andrea Alegre-Martí
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Barcelona, Spain
| | - Thierry Fischer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB/CSIC), Campus Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Ana Gradillas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | | | - Felipe Were
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Zhiqiang Huang
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Pablo Hernansanz-Agustín
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Carmen Contreras
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Fernando Martínez
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Emilio Camafeita
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jesús Vázquez
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jesús Ruiz-Cabello
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense Madrid (UCM), Madrid, Spain
| | - Estela Area-Gómez
- Departament of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Department of Neurology, Columbia University Medical Campus, New York, NY, USA
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Eckardt Treuter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juan Pedro Bolaños
- Institute of Functional Biology and Genomics (IBFG), University of Salamanca, CSIC, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Eva Estébanez-Perpiñá
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Barcelona, Spain
| | - Francisco Javier Rupérez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - José Antonio Enríquez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Mercedes Ricote
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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Burzynska-Pedziwiatr I, Dudzik D, Sansone A, Malachowska B, Zieleniak A, Zurawska-Klis M, Ferreri C, Chatgilialoglu C, Cypryk K, Wozniak LA, Markuszewski MJ, Bukowiecka-Matusiak M. Targeted and untargeted metabolomic approach for GDM diagnosis. Front Mol Biosci 2023; 9:997436. [PMID: 36685282 PMCID: PMC9849575 DOI: 10.3389/fmolb.2022.997436] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023] Open
Abstract
Gestational diabetes mellitus (GDM) is a disorder which manifests itself for the first time during pregnancy and is mainly connected with glucose metabolism. It is also known that fatty acid profile changes in erythrocyte membranes and plasma could be associated with obesity and insulin resistance. These factors can lead to the development of diabetes. In the reported study, we applied the untargeted analysis of plasma in GDM against standard glucose-tolerant (NGT) women to identify the differences in metabolomic profiles between those groups. We found higher levels of 2-hydroxybutyric and 3-hydroxybutyric acids. Both secondary metabolites are associated with impaired glucose metabolism. However, they are products of different metabolic pathways. Additionally, we applied lipidomic profiling using gas chromatography to examine the fatty acid composition of cholesteryl esters in the plasma of GDM patients. Among the 14 measured fatty acids characterizing the representative plasma lipidomic cluster, myristic, oleic, arachidonic, and α-linoleic acids revealed statistically significant changes. Concentrations of both myristic acid, one of the saturated fatty acids (SFAs), and oleic acid, which belong to monounsaturated fatty acids (MUFAs), tend to decrease in GDM patients. In the case of polyunsaturated fatty acids (PUFAs), some of them tend to increase (e.g., arachidonic), and some of them tend to decrease (e.g., α-linolenic). Based on our results, we postulate the importance of hydroxybutyric acid derivatives, cholesteryl ester composition, and the oleic acid diminution in the pathophysiology of GDM. There are some evidence suggests that the oleic acid can have the protective role in diabetes onset. However, metabolic alterations that lead to the onset of GDM are complex; therefore, further studies are needed to confirm our observations.
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Affiliation(s)
| | - Danuta Dudzik
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Anna Sansone
- Consiglio Nazionale delle Ricerche, Institute for the Organic Synthesis and Photoreactivity, Bologna, Italy
| | - Beata Malachowska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland,Department of Nursing and Obstetrics, Medical University of Lodz, Lodz, Poland,Department of Clinic Nursing, Medical University of Lodz, Lodz, Poland,Department of Diabetology and Metabolic Diseases Lodz, Medical University of Lodz, Lodz, Poland
| | - Andrzej Zieleniak
- Laboratory of Metabolomic Studies, Department of Structural Biology, Medical University of Lodz, Lodz, Poland
| | - Monika Zurawska-Klis
- Department of Radiation Oncology, Einstein College of Medicine, Bronx, NY, United States
| | - Carla Ferreri
- Consiglio Nazionale delle Ricerche, Institute for the Organic Synthesis and Photoreactivity, Bologna, Italy
| | | | - Katarzyna Cypryk
- Department of Radiation Oncology, Einstein College of Medicine, Bronx, NY, United States
| | - Lucyna A. Wozniak
- Laboratory of Metabolomic Studies, Department of Structural Biology, Medical University of Lodz, Lodz, Poland
| | - Michal J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Malgorzata Bukowiecka-Matusiak
- Laboratory of Metabolomic Studies, Department of Structural Biology, Medical University of Lodz, Lodz, Poland,*Correspondence: Malgorzata Bukowiecka-Matusiak,
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14
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de Carvalho LC, de Almeida Junior A, Ribeiro FS, Angolini CFF. Unveiling Microbial Chemical Interactions Based on Metabolomics Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:51-70. [PMID: 37843805 DOI: 10.1007/978-3-031-41741-2_3] [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: 10/17/2023]
Abstract
Microorganisms are ubiquitous in diverse habitats and studying their chemical interactions with the environment and comprehend its complex relations with both hosts and environment, are crucial for the development of strategies to control microbial diseases. This chapter discusses the importance of studying microorganisms with agricultural benefits, using specialized metabolites as examples. Herein we highlight the challenges and opportunities in utilizing microorganisms as alternatives to synthetic pesticides and fertilizers in agriculture. Genome-guided investigations and improved analytical methodologies are necessary to characterize diverse and complex biomolecules produced by microorganisms. Predicting and isolating bioproducts based on genetic information have become a focus for researchers, aided by tools like antiSMASH, BiG-SCAPE, PRISM, and others. However, translating genomic data into practical applications can be complex. Therefore, integrating genomics, transcriptomics, and metabolomics enhances chemical characterization, aiding in discovering new metabolic pathways and specialized metabolites. Additionally, elicitation is one promising strategy to enhance beneficial metabolite production. Finally, identify and characterize microbial secondary metabolites remain challenging due to their low production, complex chemical structure characterization and different environmental factors necessary for metabolite in vitro production.
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Affiliation(s)
- Laís Castro de Carvalho
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil
| | - Arnaldo de Almeida Junior
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil
| | - Fernanda Silva Ribeiro
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil
| | - Célio Fernando Figueiredo Angolini
- Mass Spectrometry and Chemical Ecology Laboratory (MC-CELL), Center for Natural and Human Sciences, University of ABC (UFABC), São Paulo, Brazil.
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15
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Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids. mSphere 2022; 7:e0018422. [PMID: 36416553 PMCID: PMC9769657 DOI: 10.1128/msphere.00184-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is one of the major threats to public health worldwide. The mechanisms involved in the plasmid/host coadaptation are still poorly characterized, and their understanding is crucial to comprehend the genesis and evolution of multidrug-resistant bacteria. With this purpose, we designed an experimental evolution using Haemophilus influenzae RdKW20 as the model strain carrying the ColE1-like plasmid pB1000. Five H. influenzae populations adapted previously to the culture conditions were transformed with pB1000 and subsequently evolved to compensate for the plasmid-associated fitness cost. Afterward, we performed an integrative multiomic analysis combining genomics, transcriptomics, and metabolomics to explore the molecular mechanisms involved in the compensatory evolution of the plasmid. Our results demonstrate that minimal modifications in the host are responsible for plasmid adaptation. Among all of them, the most enriched process was amino acid metabolism, especially those pathways related to serine, tryptophan, and arginine, eventually related to the genesis and resolution of plasmid dimers. Additional rearrangements occurred during the plasmid adaptation, such as an overexpression of the ribonucleotide reductases and metabolic modifications within specific membrane phospholipids. All these findings demonstrate that the plasmid compensation occurs through the combination of diverse host-mediated mechanisms, of which some are beyond genomic and transcriptomic modifications. IMPORTANCE The ability of bacteria to horizontally transfer genetic material has turned antimicrobial resistance into one of the major sanitary crises of the 21st century. Plasmid conjugation is considered the main mechanism responsible for the mobilization of resistance genes, and its understanding is crucial to tackle this crisis. It is generally accepted that the acquisition and maintenance of mobile genetic elements entail a fitness cost to its host, which is susceptible to be alleviated through a coadaptation process or compensatory evolution. Notwithstanding, despite recent major efforts, the underlying mechanisms involved in this adaptation remain poorly characterized. Analyzing the plasmid/host coadaptation from a multiomic perspective sheds light on the physiological processes involved in the compensation, providing a new understanding on the genesis and evolution of plasmid-mediated antimicrobial-resistant bacteria.
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16
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Comprehensive Controller for Super Sonic Molecular Beam Gas Chromatograph Mass Spectrometer. SEPARATIONS 2022. [DOI: 10.3390/separations9120417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This paper presents a new, comprehensive digital circuit used for the control of a novel gas chromatograph mass spectrometer (GC-MS) interface that is based on supersonic molecular beam (SMB). The circuit includes a Texas Instruments 150 MHz digital signal controller (DSC), high voltage amplifiers for 8 independent channels and 4 independent channels of high resolution pulse width modulation (PWM). The circuit, along with a sophisticated embedded program and a custom made personal computer (PC) application, control all aspects of the interface: smart filament emission-current stabilization, static and scanning mass-dependent ion-source voltages, transfer-line heater proportional integral differential (PID) controls with thermocouple feedbacks, on/off valves, relays and several peripheral device controls that enable the full operation of a turbo-molecular vacuum pump, and of gas flow and pressure controllers. All aspects of this comprehensive controller were successfully tested. The signal for the 450 Th ion (C32H66) for example increased by 123% which is a significant increase. It is obvious that correctly tuned dynamic voltages can guarantee the optimal signal for each mass.
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