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Oesterle I, Ayeni KI, Ezekiel CN, Berry D, Rompel A, Warth B. Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome. ENVIRONMENT INTERNATIONAL 2024; 188:108766. [PMID: 38801800 DOI: 10.1016/j.envint.2024.108766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides, although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin elevated as complementary foods were introduced to the infants' diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.
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Affiliation(s)
- Ian Oesterle
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, 1090 Vienna, Austria; Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, 1090 Wien, Austria(1); University of Vienna, Vienna Doctoral School of Chemistry (DoSChem), 1090 Vienna, Austria
| | - Kolawole I Ayeni
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, 1090 Vienna, Austria; Department of Microbiology, Babcock University, Ilishan-Remo, Ogun State, Nigeria
| | - Chibundu N Ezekiel
- Department of Microbiology, Babcock University, Ilishan-Remo, Ogun State, Nigeria; University of Natural Resources and Life Sciences Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Institute for Bioanalytics and Agro-Metabolomics, Konrad-Lorenz Str. 20, 3430 Tulln, Austria
| | - David Berry
- University of Vienna, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, 1030 Vienna, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, 1090 Wien, Austria(1); University of Vienna, Vienna Doctoral School of Chemistry (DoSChem), 1090 Vienna, Austria
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, 1090 Vienna, Austria; University of Vienna, Vienna Doctoral School of Chemistry (DoSChem), 1090 Vienna, Austria; Exposome Austria, Research Infrastructure and National EIRENE Node, Austria.
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2
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Foreman AL, Warth B, Hessel EVS, Price EJ, Schymanski EL, Cantelli G, Parkinson H, Hecht H, Klánová J, Vlaanderen J, Hilscherova K, Vrijheid M, Vineis P, Araujo R, Barouki R, Vermeulen R, Lanone S, Brunak S, Sebert S, Karjalainen T. Adopting Mechanistic Molecular Biology Approaches in Exposome Research for Causal Understanding. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7256-7269. [PMID: 38641325 PMCID: PMC11064223 DOI: 10.1021/acs.est.3c07961] [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: 09/25/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Through investigating the combined impact of the environmental exposures experienced by an individual throughout their lifetime, exposome research provides opportunities to understand and mitigate negative health outcomes. While current exposome research is driven by epidemiological studies that identify associations between exposures and effects, new frameworks integrating more substantial population-level metadata, including electronic health and administrative records, will shed further light on characterizing environmental exposure risks. Molecular biology offers methods and concepts to study the biological and health impacts of exposomes in experimental and computational systems. Of particular importance is the growing use of omics readouts in epidemiological and clinical studies. This paper calls for the adoption of mechanistic molecular biology approaches in exposome research as an essential step in understanding the genotype and exposure interactions underlying human phenotypes. A series of recommendations are presented to make the necessary and appropriate steps to move from exposure association to causation, with a huge potential to inform precision medicine and population health. This includes establishing hypothesis-driven laboratory testing within the exposome field, supported by appropriate methods to read across from model systems research to human.
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Affiliation(s)
- Amy L. Foreman
- European
Molecular Biology Laboratory & European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K.
| | - Benedikt Warth
- Department
of Food Chemistry and Toxicology, University
of Vienna, 1090 Vienna, Austria
| | - Ellen V. S. Hessel
- National
Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Elliott J. Price
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Emma L. Schymanski
- Luxembourg
Centre for Systems Biomedicine, University
of Luxembourg, 6 avenue
du Swing, L-4367 Belvaux, Luxembourg
| | - Gaia Cantelli
- European
Molecular Biology Laboratory & European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K.
| | - Helen Parkinson
- European
Molecular Biology Laboratory & European Bioinformatics Institute
(EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K.
| | - Helge Hecht
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Jana Klánová
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Jelle Vlaanderen
- Institute
for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Heidelberglaan 8 3584 CS Utrecht, The Netherlands
| | - Klara Hilscherova
- RECETOX,
Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Martine Vrijheid
- Institute
for Global Health (ISGlobal), Barcelona
Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat
Pompeu Fabra, Carrer
de la Mercè, 12, Ciutat Vella, 08002 Barcelona, Spain
- Centro de Investigación Biomédica en Red
Epidemiología
y Salud Pública (CIBERESP), Av. Monforte de Lemos, 3-5. Pebellón 11, Planta 0, 28029 Madrid, Spain
| | - Paolo Vineis
- Department
of Epidemiology and Biostatistics, School of Public Health, Imperial College, London SW7 2AZ, U.K.
| | - Rita Araujo
- European Commission, DG Research and Innovation, Sq. Frère-Orban 8, 1000 Bruxelles, Belgium
| | | | - Roel Vermeulen
- Institute
for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Heidelberglaan 8 3584 CS Utrecht, The Netherlands
| | - Sophie Lanone
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France
| | - Søren Brunak
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Blegdamsvej 3B, 2200 København, Denmark
| | - Sylvain Sebert
- Research
Unit of Population Health, University of
Oulu, P.O. Box 8000, FI-90014 Oulu, Finland
| | - Tuomo Karjalainen
- European Commission, DG Research and Innovation, Sq. Frère-Orban 8, 1000 Bruxelles, Belgium
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Balcells C, Xu Y, Gil-Solsona R, Maitre L, Gago-Ferrero P, Keun HC. Blurred lines: Crossing the boundaries between the chemical exposome and the metabolome. Curr Opin Chem Biol 2024; 78:102407. [PMID: 38086287 DOI: 10.1016/j.cbpa.2023.102407] [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: 08/21/2023] [Revised: 10/22/2023] [Accepted: 11/09/2023] [Indexed: 02/09/2024]
Abstract
The aetiology of every human disease lies in a combination of genetic and environmental factors, each contributing in varying proportions. While genomics investigates the former, a comparable holistic paradigm was proposed for environmental exposures in 2005, marking the onset of exposome research. Since then, the exposome definition has broadened to include a wide array of physical, chemical, and psychosocial factors that interact with the human body and potentially alter the epigenome, the transcriptome, the proteome, and the metabolome. The chemical exposome, deeply intertwined with the metabolome, includes all small molecules originating from diet as well as pharmaceuticals, personal care and consumer products, or pollutants in air and water. The set of techniques to interrogate these exposures, primarily mass spectrometry and nuclear magnetic resonance spectroscopy, are also extensively used in metabolomics. Recent advances in untargeted metabolomics using high resolution mass spectrometry have paved the way for the development of methods able to provide in depth characterisation of both the internal chemical exposome and the endogenous metabolome simultaneously. Herein we review the available tools, databases, and workflows currently available for such work, and discuss how these can bridge the gap between the study of the metabolome and the exposome.
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Affiliation(s)
- Cristina Balcells
- Institute of Developmental and Reproductive Biology (IRDB), Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
| | - Yitao Xu
- Institute of Developmental and Reproductive Biology (IRDB), Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Rubén Gil-Solsona
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - Léa Maitre
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Pablo Gago-Ferrero
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - Hector C Keun
- Institute of Developmental and Reproductive Biology (IRDB), Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
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Goracci L, Tiberi P, Di Bona S, Bonciarelli S, Passeri GI, Piroddi M, Moretti S, Volpi C, Zamora I, Cruciani G. MARS: A Multipurpose Software for Untargeted LC-MS-Based Metabolomics and Exposomics. Anal Chem 2024; 96:1468-1477. [PMID: 38236168 PMCID: PMC10831794 DOI: 10.1021/acs.analchem.3c03620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/19/2024]
Abstract
Untargeted metabolomics is a growing field, in which recent advances in high-resolution mass spectrometry coupled with liquid chromatography (LC-MS) have facilitated untargeted approaches as a result of improvements in sensitivity, mass accuracy, and resolving power. However, a very large amount of data are generated. Consequently, using computational tools is now mandatory for the in-depth analysis of untargeted metabolomics data. This article describes MetAbolomics ReSearch (MARS), an all-in-one vendor-agnostic graphical user interface-based software applying LC-MS analysis to untargeted metabolomics. All of the analytical steps are described (from instrument data conversion and processing to statistical analysis, annotation/identification, quantification, and preliminary biological interpretation), and tools developed to improve annotation accuracy (e.g., multiple adducts and in-source fragmentation detection, trends across samples, and the MS/MS validator) are highlighted. In addition, MARS allows in-house building of reference databases, to bypass the limits of freely available MS/MS spectra collections. Focusing on the flexibility of the software and its user-friendliness, which are two important features in multipurpose software, MARS could provide new perspectives in untargeted metabolomics data analysis.
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Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, Universita degli Studi di Perugia, via Elce di Sotto 8, Perugia 06123, Italy
| | - Paolo Tiberi
- Molecular
Discovery Ltd., Centennial
Park, Borehamwood, Hertfordshire WD6 4PJ, U.K.
| | - Stefano Di Bona
- Molecular
Horizon, Via Montelino,
30, Bettona (PG) 06084, Italy
| | - Stefano Bonciarelli
- Molecular
Discovery Ltd., Centennial
Park, Borehamwood, Hertfordshire WD6 4PJ, U.K.
| | | | - Marta Piroddi
- Molecular
Horizon, Via Montelino,
30, Bettona (PG) 06084, Italy
| | - Simone Moretti
- Molecular
Horizon, Via Montelino,
30, Bettona (PG) 06084, Italy
| | - Claudia Volpi
- Department
of Medicine and Surgery, P.le Gambuli 1, Perugia 06129, Italy
| | - Ismael Zamora
- Mass
Analytica, Rambla de
celler 113, Sant Cugat del Vallés 08173, Spain
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, Universita degli Studi di Perugia, via Elce di Sotto 8, Perugia 06123, Italy
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Ayeni KI, Jamnik T, Fareed Y, Flasch M, Braun D, Uhl M, Hartmann C, Warth B. The Austrian children's biomonitoring survey 2020 Part B: Mycotoxins, phytotoxins, phytoestrogens and food processing contaminants. Food Chem Toxicol 2023; 182:114173. [PMID: 37925015 DOI: 10.1016/j.fct.2023.114173] [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: 06/16/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023]
Abstract
This study assessed the levels of environment and food-related exposures in urine of Austrian school children aged six to ten (n = 85) focusing on mycotoxins, phytoestrogens, and food processing by-products using two multi-analyte LC-MS/MS methods. Out of the 55 biomarkers of exposure reported in this study, 22 were quantified in the first void urine samples. Mycotoxins frequently quantified included zearalenone (detection rate 100%; median 0.11 ng/mL), deoxynivalenol (99%; 15 ng/mL), alternariol monomethyl ether (75%; 0.04 ng/mL), and ochratoxin A (19%; 0.03 ng/mL). Several phytoestrogens, including genistein, daidzein, and its metabolite equol, were detected in all samples at median concentrations of 22 ng/mL, 43 ng/mL, and 14 ng/mL, respectively. The food processing by-product 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), was detected in 4% of the samples (median 0.016 ng/mL). None of the investigated samples contained the tested phytotoxins that were rarely considered for human biomonitoring previously (pyrrolizidine alkaloids, tropane alkaloids, aristolochic acids). When relating estimated exposure to current health-based guidance values, 22% of the children exceeded the tolerable daily intake for deoxynivalenol, and the estimated MOE for OTA indicates possible health risks for some children. The results clearly demonstrate frequent low-level (co-)exposure and warrant further exposome-scale exposure assessments, especially in susceptible sub-populations and longitudinal settings.
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Affiliation(s)
- Kolawole I Ayeni
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria; Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - Thomas Jamnik
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Yasmin Fareed
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Mira Flasch
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Dominik Braun
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Maria Uhl
- Environment Agency Austria (Umweltbundesamt GmbH), Spittelauer Lände 5, 1090, Vienna, Austria; Exposome Austria, Research Infrastructure and National EIRENE Node, Austria
| | - Christina Hartmann
- Environment Agency Austria (Umweltbundesamt GmbH), Spittelauer Lände 5, 1090, Vienna, Austria
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria; Exposome Austria, Research Infrastructure and National EIRENE Node, Austria.
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Gao P. Exploring Single-Cell Exposomics by Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12201-12209. [PMID: 37561608 PMCID: PMC10448745 DOI: 10.1021/acs.est.3c04524] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Indexed: 08/12/2023]
Abstract
Single-cell exposomics, a revolutionary approach that investigates cell-environment interactions at cellular and subcellular levels, stands distinct from conventional bulk exposomics. Leveraging advancements in mass spectrometry, it provides a detailed perspective on cellular dynamics, interactions, and responses to environmental stimuli and their impacts on human health. This work delves into this innovative realm, highlighting the nuanced interplay between environmental stressors and biological responses at cellular and subcellular levels. The application of spatial mass spectrometry in single-cell exposomics is discussed, revealing the intricate spatial organization and molecular composition within individual cells. Cell-type-specific exposomics, shedding light on distinct susceptibilities and adaptive strategies of various cell types to environmental exposures, is also examined. The Perspective further emphasizes the integration with molecular and cellular biology approaches to validate hypotheses derived from single-cell exposomics in a comprehensive biological context. Looking toward the future, we anticipate continued technological advancements and convergence with other -omics approaches and discuss implications for environmental health research, disease progression studies, and precision medicine. The final emphasis is on the need for robust computational tools and interdisciplinary collaboration to fully leverage the potential of single-cell exposomics, acknowledging the complexities inherent to this paradigm.
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Affiliation(s)
- Peng Gao
- Department
of Environmental and Occupational Health and Department of Civil and
Environmental Engineering, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- UPMC
Hillman Cancer Center, Pittsburgh, Pennsylvania 15232, United States
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