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Magny R, Lefrère B, Roulland E, Auzeil N, Farah S, Richeval C, Gish A, Vodovar D, Labat L, Houzé P. Feature-Based Molecular Network for New Psychoactive Substance Identification: The Case of Synthetic Cannabinoids in a Seized e-Liquid and Biological Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39186500 DOI: 10.1021/jasms.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
The comprehensive detection of new psychoactive substances, including synthetic cannabinoids along with their associated metabolites in biological samples, remains an analytical challenge. To detect these chemicals, untargeted approaches using appropriate bioinformatic tools such as molecular networks are useful, albeit it necessitates as a prerequisite the identification of a node of interest within the cluster. To illustrate it, we reported in this study the identification of synthetic cannabinoids and some of their metabolites in seized e-liquid, urine, and hair collected from an 18-year-old poisoned patient hospitalized for neuropsychiatric disorders. A comprehensive analysis of the seized e-liquid was performed using gas chromatography coupled with electron ionization mass spectrometry, 1H NMR, and liquid chromatography coupled with high resolution tandem mass spectrometry combined with data processing based on molecular network strategy. It allowed researchers to detect in the e-liquid known synthetic cannabinoids including MDMB-4en-PINACA, EDMB-4en-PINACA, MMB-4en-PINACA, and MDMB-5F-PICA. Compounds corresponding to transesterification of MDMB-4en-PINACA with pentenol, glycerol, and propylene glycol were also identified. Regarding the urine sample of the patient, metabolites of MDMB-4en-PINACA were detected, including MDMB-4en-PINACA butanoic acid, dihydroxylated MDMB-4en-PINACA butanoic acid, and glucurono-conjugated MDMB-4en-PINACA butanoic acid. Hair analysis of the patient allowed the detection of MDMB-4en-PINACA and MDMB-5F-PICA in the two investigated hair segments. This untargeted analysis of seized materials and biological samples demonstrates the utility of the molecular network strategy in identifying closely related compounds and metabolites of synthetic cannabinoids. It also emphasizes the need for developing strategies to anchor molecular networks, especially for new psychoactive substances.
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Affiliation(s)
- Romain Magny
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
| | - Bertrand Lefrère
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
| | | | - Nicolas Auzeil
- CNRS, CiTCoM, Université Paris Cité, 75006 Paris, France
| | - Soha Farah
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
| | - Camille Richeval
- CHRU Lille, Unité Fonctionnelle de Toxicologie, 59000 Lille, France
- ULR 4483-IMPECS-IMPact de l'Environnement Chimique sur la Santé humaine, Université de Lille, 59000 Lille, France
| | - Alexandr Gish
- CHRU Lille, Unité Fonctionnelle de Toxicologie, 59000 Lille, France
- ULR 4483-IMPECS-IMPact de l'Environnement Chimique sur la Santé humaine, Université de Lille, 59000 Lille, France
| | - Dominique Vodovar
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
- Centre antipoison de Paris, Hôpital Fernand Widal, AP-HP, 75010 Paris, France
| | - Laurence Labat
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
| | - Pascal Houzé
- Laboratoire de Toxicologie, Fédération de Toxicologie, AH-HP, Hôpital Lariboisière, 75010 Paris, France
- INSERM UMRS-1144, Université Paris Cité, 75006 Paris, France
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2
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Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus). mSystems 2024; 9:e0010824. [PMID: 38975760 PMCID: PMC11334461 DOI: 10.1128/msystems.00108-24] [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: 01/26/2024] [Accepted: 06/01/2024] [Indexed: 07/09/2024] Open
Abstract
Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change. IMPORTANCE Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.
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Affiliation(s)
- Cassandra Tang-Wing
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Katherine Makowski
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Daira Melendez
- Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Keith Jenné
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
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3
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Dablanc A, Hennechart S, Perez A, Cabanac G, Guitton Y, Paulhe N, Lyan B, Jamin EL, Giacomoni F, Marti G. FragHub: A Mass Spectral Library Data Integration Workflow. Anal Chem 2024; 96. [PMID: 39028894 PMCID: PMC11295123 DOI: 10.1021/acs.analchem.4c02219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 07/21/2024]
Abstract
Open mass spectral libraries (OMSLs) are critical for metabolite annotation and machine learning, especially given the rising volume of untargeted metabolomic studies and the development of annotation pipelines. Despite their importance, the practical application of OMSLs is hampered by the lack of standardized file formats, metadata fields, and supporting ontology. Current libraries, often restricted to specific topics or matrices, such as natural products, lipids, or the human metabolome, may limit the discovery potential of untargeted studies. The goal of FragHub is to provide users with the capability to integrate various OMSLs into a single unified format, thereby enhancing the annotation accuracy and reliability. FragHub addresses these challenges by integrating multiple OMSLs into a single comprehensive database, supporting various data formats, and harmonizing metadata. It also proposes some generic filters for the mass spectrum using a graphical user interface. Additionally, a workflow to generate in-house libraries compatible with FragHub is proposed. FragHub dynamically segregates libraries based on ionization modes and chromatography techniques, thereby enhancing data utility in metabolomic research. The FragHub Python code is publicly available under a MIT license, at the following repository: https://github.com/eMetaboHUB/FragHub. Generated data can be accessed at 10.5281/zenodo.11057687.
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Affiliation(s)
- Axel Dablanc
- Laboratoire
de Recherche en Sciences Végétales, Metatoul-AgromiX
Platform, Université de Toulouse,
CNRS, INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- MetaboHUB-MetaToul,
National Infrastructure of Metabolomics and Fluxomics, Toulouse 31000, France
| | - Solweig Hennechart
- Laboratoire
de Recherche en Sciences Végétales, Metatoul-AgromiX
Platform, Université de Toulouse,
CNRS, INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- MetaboHUB-MetaToul,
National Infrastructure of Metabolomics and Fluxomics, Toulouse 31000, France
- Université
Toulouse 3—Paul Sabatier, IRIT UMR 5505 CNRS, Toulouse 31062, France
| | - Amélie Perez
- Laboratoire
de Recherche en Sciences Végétales, Metatoul-AgromiX
Platform, Université de Toulouse,
CNRS, INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- MetaboHUB-MetaToul,
National Infrastructure of Metabolomics and Fluxomics, Toulouse 31000, France
| | - Guillaume Cabanac
- Université
Toulouse 3—Paul Sabatier, IRIT UMR 5505 CNRS, Toulouse 31062, France
- Institut
Universitaire de France, Paris 75005, France
| | | | - Nils Paulhe
- Université
Clermont Auvergne, INRAE, UNH, Plateforme d’Exploration du
Métabolisme, MetaboHUB Clermont, Clermont-Ferrand F-63000, France
| | - Bernard Lyan
- Université
Clermont Auvergne, INRAE, UNH, Plateforme d’Exploration du
Métabolisme, MetaboHUB Clermont, Clermont-Ferrand F-63000, France
| | - Emilien L. Jamin
- MetaboHUB-MetaToul,
National Infrastructure of Metabolomics and Fluxomics, Toulouse 31000, France
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse 31076, France
| | - Franck Giacomoni
- Université
Clermont Auvergne, INRAE, UNH, Plateforme d’Exploration du
Métabolisme, MetaboHUB Clermont, Clermont-Ferrand F-63000, France
| | - Guillaume Marti
- Laboratoire
de Recherche en Sciences Végétales, Metatoul-AgromiX
Platform, Université de Toulouse,
CNRS, INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- MetaboHUB-MetaToul,
National Infrastructure of Metabolomics and Fluxomics, Toulouse 31000, France
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4
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Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nat Rev Gastroenterol Hepatol 2024; 21:493-516. [PMID: 38575682 DOI: 10.1038/s41575-024-00914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/06/2024]
Abstract
Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The observation that there are hundreds of bile acids, especially many amidated bile acids, necessitates a revision of many of the classical descriptions of bile acids and bile acid enzyme functions. For example, bile salt hydrolases also have transferase activity. There are now hundreds of known modifications to bile acids and thousands of bile acid-associated genes, especially when including the microbiome, distributed throughout the human body (for example, there are >2,400 bile salt hydrolases alone). The fact that so much of our genetic and small-molecule repertoire, in both amount and diversity, is dedicated to bile acid function highlights the centrality of bile acids as key regulators of metabolism and immune homeostasis, which is, in large part, communicated via the gut microbiome.
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Affiliation(s)
- Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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5
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Fan Z, Jia W. High-confidence structural annotation of substances via multi-layer molecular network reveals the system-wide constituent alternations in milk interfered with diphenylolpropane. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134334. [PMID: 38642498 DOI: 10.1016/j.jhazmat.2024.134334] [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: 02/24/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
The spectral database-based mass spectrometry (MS) matching strategy is versatile for structural annotating in ingredient fluctuation profiling mediated by external interferences. However, the systematic variability of MS pool attributable to aliasing peaks and inadequacy of present spectral database resulted in a substantial metabolic feature depletion. An amended procedure termed multiple-charges overlap peaks extraction algorithm (MCOP) was proposed involving identifying collision-trigged dissociation precursor ions through iteratively matching mass features of fragmentations to expand the spectral reference library. We showcased the versatility and utility of established strategy in an investigation centered on the stimulation of milk mediated by diphenylolpropane (BPA). MCOP enabled efficient unknown annotations at metabolite-lipid-protein level, which elevated the accuracy of substance annotation to 85.3% after manual validation. Arginase and α-amylase (|r| > 0.75, p < 0.05) were first identified as the crucial issues via graph neural network-based virtual screening in the abnormal metabolism of urea triggered by BPA, resulting in the accumulation of arginine (original: 1.7 μg kg-1 1.7 times) and maltodextrin (original: 6.9 μg kg-1 2.9 times) and thus, exciting the potential dietary risks. Conclusively, MCOP demonstrated generalisation and scalability and substantially advanced the discovery of unknown metabolites for complex matrix samples, thus deciphering dark matter in multi-omics.
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Affiliation(s)
- Zibian Fan
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Wei Jia
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Shaanxi Research Institute of Agricultural Products Processing Technology, Xi'an 710021, China.
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6
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Zahn D, Arp HPH, Fenner K, Georgi A, Hafner J, Hale SE, Hollender J, Letzel T, Schymanski EL, Sigmund G, Reemtsma T. Should Transformation Products Change the Way We Manage Chemicals? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7710-7718. [PMID: 38656189 PMCID: PMC11080041 DOI: 10.1021/acs.est.4c00125] [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: 01/04/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
When chemical pollutants enter the environment, they can undergo diverse transformation processes, forming a wide range of transformation products (TPs), some of them benign and others more harmful than their precursors. To date, the majority of TPs remain largely unrecognized and unregulated, particularly as TPs are generally not part of routine chemical risk or hazard assessment. Since many TPs formed from oxidative processes are more polar than their precursors, they may be especially relevant in the context of persistent, mobile, and toxic (PMT) and very persistent and very mobile (vPvM) substances, which are two new hazard classes that have recently been established on a European level. We highlight herein that as a result, TPs deserve more attention in research, chemicals regulation, and chemicals management. This perspective summarizes the main challenges preventing a better integration of TPs in these areas: (1) the lack of reliable high-throughput TP identification methods, (2) uncertainties in TP prediction, (3) inadequately considered TP formation during (advanced) water treatment, and (4) insufficient integration and harmonization of TPs in most regulatory frameworks. A way forward to tackle these challenges and integrate TPs into chemical management is proposed.
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Affiliation(s)
- Daniel Zahn
- Helmholtz
Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Peter H. Arp
- Norwegian
Geotechnical Institute (NGI), P.O. Box 3930, Ullevål Stadion, 0806 Oslo, Norway
- Department
of Chemistry, Norwegian University of Science
and Technology (NTNU), N-7491 Trondheim, Norway
| | - Kathrin Fenner
- Swiss
Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
- Department
of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Anett Georgi
- Helmholtz
Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Jasmin Hafner
- Swiss
Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
- Department
of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Sarah E. Hale
- TZW: DVGW
Water Technology Center, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Juliane Hollender
- Swiss
Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
- ETH
Zurich, Institute of Biogeochemistry and
Pollutant Dynamics, Zürich 8092, Switzerland
| | - Thomas Letzel
- AFIN-TS
GmbH (Analytisches Forschungsinstitut für Non-Target Screening), Am Mittleren Moos 48, 86167 Augsburg, Germany
| | - Emma L. Schymanski
- Luxembourg
Centre for Systems Biomedicine (LCSB), University
of Luxembourg, 6 avenue
du Swing, L-4367 Belvaux, Luxembourg
| | - Gabriel Sigmund
- Environmental
Technology, Wageningen University &
Research, 6700 AA Wageningen, The Netherlands
| | - Thorsten Reemtsma
- Helmholtz
Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
- University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
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7
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Yan T, Nie L, Hao H. Reverse metabolomics as a novel strategy to annotate the human metabolome. Chin J Nat Med 2024; 22:289-290. [PMID: 38658091 DOI: 10.1016/s1875-5364(24)60589-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Tingting Yan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; Laboratory of Metabolic Regulation and Drug Target Discovery, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Liangliang Nie
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; Laboratory of Metabolic Regulation and Drug Target Discovery, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; Laboratory of Metabolic Regulation and Drug Target Discovery, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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8
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Mohanty I, Mannochio-Russo H, Schweer JV, El Abiead Y, Bittremieux W, Xing S, Schmid R, Zuffa S, Vasquez F, Muti VB, Zemlin J, Tovar-Herrera OE, Moraïs S, Desai D, Amin S, Koo I, Turck CW, Mizrahi I, Kris-Etherton PM, Petersen KS, Fleming JA, Huan T, Patterson AD, Siegel D, Hagey LR, Wang M, Aron AT, Dorrestein PC. The underappreciated diversity of bile acid modifications. Cell 2024; 187:1801-1818.e20. [PMID: 38471500 DOI: 10.1016/j.cell.2024.02.019] [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: 04/26/2023] [Revised: 11/30/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.
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Affiliation(s)
- Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Joshua V Schweer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium
| | - Shipei Xing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, Vancouver, BC, Canada
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Felipe Vasquez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Valentina B Muti
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, USA; Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar E Tovar-Herrera
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Dhimant Desai
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - Shantu Amin
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - Imhoi Koo
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Kraepelinstrasse 2-10, Munich 80804, Germany; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Penny M Kris-Etherton
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Kristina S Petersen
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jennifer A Fleming
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, Vancouver, BC, Canada
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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Martin MR, Bittremieux W, Hassoun S. Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578795. [PMID: 38370723 PMCID: PMC10871291 DOI: 10.1101/2024.02.04.578795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Although untargeted mass spectrometry-based metabolomics is crucial for understanding life's molecular underpinnings, its effectiveness is hampered by low annotation rates of the generated tandem mass spectra. To address this issue, we introduce a novel data-driven approach, Biotransformation-based Annotation Method (BAM), that leverages molecular structural similarities inherent in biochemical reactions. BAM operates by applying biotransformation rules to known 'anchor' molecules, which exhibit high spectral similarity to unknown spectra, thereby hypothesizing and ranking potential structures for the corresponding 'suspect' molecule. BAM's effectiveness is demonstrated by its success in annotating suspect spectra in a global molecular network comprising hundreds of millions of spectra. BAM was able to assign correct molecular structures to 24.2 % of examined anchor-suspect cases, thereby demonstrating remarkable advancement in metabolite annotation.
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