1
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Rhein S, Costalunga R, Inderhees J, Gürtzgen T, Faupel TC, Shaheryar Z, Arrulo Pereira A, Othman A, Begemann K, Binder S, Stölting I, Dorta V, Nawroth PP, Fleming T, Oexle K, Prevot V, Nogueiras R, Meyhöfer S, Meyhöfer SM, Schwaninger M. The reactive pyruvate metabolite dimethylglyoxal mediates neurological consequences of diabetes. Nat Commun 2024; 15:5745. [PMID: 38987239 PMCID: PMC11237006 DOI: 10.1038/s41467-024-50089-3] [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: 07/20/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Complications of diabetes are often attributed to glucose and reactive dicarbonyl metabolites derived from glycolysis or gluconeogenesis, such as methylglyoxal. However, in the CNS, neurons and endothelial cells use lactate as energy source in addition to glucose, which does not lead to the formation of methylglyoxal and has previously been considered a safer route of energy consumption than glycolysis. Nevertheless, neurons and endothelial cells are hotspots for the cellular pathology underlying neurological complications in diabetes, suggesting a cause that is distinct from other diabetes complications and independent of methylglyoxal. Here, we show that in clinical and experimental diabetes plasma concentrations of dimethylglyoxal are increased. In a mouse model of diabetes, ilvb acetolactate-synthase-like (ILVBL, HACL2) is the enzyme involved in formation of increased amounts of dimethylglyoxal from lactate-derived pyruvate. Dimethylglyoxal reacts with lysine residues, forms Nε-3-hydroxy-2-butanonelysine (HBL) as an adduct, induces oxidative stress more strongly than other dicarbonyls, causes blood-brain barrier disruption, and can mimic mild cognitive impairment in experimental diabetes. These data suggest dimethylglyoxal formation as a pathway leading to neurological complications in diabetes that is distinct from other complications. Importantly, dimethylglyoxal formation can be reduced using genetic, pharmacological and dietary interventions, offering new strategies for preventing CNS dysfunction in diabetes.
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Affiliation(s)
- Sina Rhein
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Riccardo Costalunga
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
- Bioanalytic Core Facility, Center for Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Julica Inderhees
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
- Bioanalytic Core Facility, Center for Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Tammo Gürtzgen
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Teresa Christina Faupel
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Zaib Shaheryar
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Adriana Arrulo Pereira
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Alaa Othman
- Bioanalytic Core Facility, Center for Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany
- Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland
| | - Kimberly Begemann
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Sonja Binder
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Ines Stölting
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Valentina Dorta
- Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de, Compostela, Spain
| | - Peter P Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Department of Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Konrad Oexle
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz, Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vincent Prevot
- Univ. Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S 1172, DISTALZ, EGID, Lille, France
| | - Ruben Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de, Compostela, Spain
| | - Svenja Meyhöfer
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
- Institute for Endocrinology and Diabetes, University of Lübeck, Lübeck, Germany
- Department of Medicine I, University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Sebastian M Meyhöfer
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
- Institute for Endocrinology and Diabetes, University of Lübeck, Lübeck, Germany
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany.
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany.
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2
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Hueber A, Kulyk H, Damont A, Nicol E, Alves S, Liuu S, Green M, Bertrand-Michel J, Cenac N, Fenaille F, Tabet JC. Energy Resolved Mass Spectrometry for Interoperable Non-resonant Collisional Spectra in Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:834-838. [PMID: 38557041 DOI: 10.1021/jasms.3c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In untargeted metabolomics, the unambiguous identification of metabolites remains a major challenge. This requires high-quality spectral libraries for reliable metabolite identification, which is essential for translating metabolomics data into meaningful biological information. Several attempts have been made to generate reproducible product ion spectra (PIS) under a low collision energy (ELab) regime and nonresonant collisional conditions but have not fully succeeded. We examined the ERMS (energy-resolved mass spectrometry) breakdown curves of two lipo-amino acids and showed the possibility to highlight "singular points", called descriptors hereafter (linked to respective ELab depending on the instrument), for each of the monomodal product ion profiles. Using several instruments based on different technologies, the PIS recorded at these specific ELab sites shows remarkable similarities. The descriptors appeared as being independent of the fragmentation mechanisms and can be used to overcome the main instrumental effects that limit the interoperability of spectral libraries. This proof-of-concept study, performed on two particular lipo-amino acids, demonstrates the high potential of ERMS-derived information to determine the instrument-specific ELab at which PIS recorded in nonresonant conditions become highly similar and instrument-independent, thus comparable across platforms. This innovative but straightforward approach could help remove some of the obstacles to metabolite identification in nontargeted metabolomics, putting an end to a challenging chimera.
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Affiliation(s)
- Amandine Hueber
- I2MC, Inserm, 31432 Toulouse, France
- IRSD, Université de Toulouse, INSERM, INRAE, INPENVT, 31024 Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
| | - Hanna Kulyk
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
| | - Sophie Liuu
- Food Safety Laboratory, ANSES, 94701 Maisons-Alfort, France
| | - Martin Green
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom
| | - Justine Bertrand-Michel
- I2MC, Inserm, 31432 Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
| | - Nicolas Cenac
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31400 Toulouse, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, 91191 Gif-sur-Yvette, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), 75005 Paris, France
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3
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Chernonosov AA, Mednova IA, Levchuk LA, Mazurenko EO, Roschina OV, Simutkin GG, Bokhan NA, Koval VV, Ivanova SA. Untargeted Plasma Metabolomic Profiling in Patients with Depressive Disorders: A Preliminary Study. Metabolites 2024; 14:110. [PMID: 38393002 PMCID: PMC10890195 DOI: 10.3390/metabo14020110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Depressive disorder is a multifactorial disease that is based on dysfunctions in mental and biological processes. The search for biomarkers can improve its diagnosis, personalize therapy, and lead to a deep understanding of the biochemical processes underlying depression. The purpose of this work was a metabolomic analysis of blood serum to classify patients with depressive disorders and healthy individuals using Compound Discoverer software. Using high-resolution mass spectrometry, blood plasma samples from 60 people were analyzed, of which 30 were included in a comparison group (healthy donors), and 30 were patients with a depressive episode (F32.11) and recurrent depressive disorder (F33.11). Differences between patient and control groups were identified using the built-in utilities in Compound Discoverer software. Compounds were identified by their accurate mass and fragment patterns using the mzCloud database and tentatively identified by their exact mass using the ChemSpider search engine and the KEGG, ChEBI, FDA UNII-NLM, Human Metabolome and LipidMAPS databases. We identified 18 metabolites that could divide patients with depressive disorders from healthy donors. Of these, only two compounds were tentatively identified using the mzCloud database (betaine and piperine) based on their fragmentation spectra. For three compounds ((4S,5S,8S,10R)-4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one, (2E,4E)-N-(2-hydroxy-2-methylpropyl)-2,4-tetradecadienamide and 17α-methyl-androstan-3-hydroxyimine-17β-ol), matches were found in the mzCloud database but with low score, which could not serve as reliable evidence of their structure. Another 13 compounds were identified by their exact mass in the ChemSpider database, 9 (g-butyrobetaine, 6-diazonio-5-oxo-L-norleucine, 11-aminoundecanoic acid, methyl N-acetyl-2-diazonionorleucinate, glycyl-glycyl-argininal, dilaurylmethylamine, 12-ketodeoxycholic acid, dicetylamine, 1-linoleoyl-2-hydroxy-sn-glycero-3-PC) had only molecular formulas proposed, and 4 were unidentified. Thus, the use of Compound Discoverer software alone was not sufficient to identify all revealed metabolites. Nevertheless, the combination of the found metabolites made it possible to divide patients with depressive disorders from healthy donors.
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Affiliation(s)
- Alexander A Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Irina A Mednova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - Lyudmila A Levchuk
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - Ekaterina O Mazurenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Olga V Roschina
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - German G Simutkin
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - Nikolay A Bokhan
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
- Department of Psychiatry, Addictology and Psychotherapy, Siberian State Medical University, Moskovsky Trakt 2, Tomsk 634050, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Svetlana A Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
- Department of Psychiatry, Addictology and Psychotherapy, Siberian State Medical University, Moskovsky Trakt 2, Tomsk 634050, Russia
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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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5
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Oelkrug R, Harder L, Pedaran M, Hoffmann A, Kolms B, Inderhees J, Gachkar S, Resch J, Johann K, Jöhren O, Krause K, Mittag J. Maternal thyroid hormone receptor β activation in mice sparks brown fat thermogenesis in the offspring. Nat Commun 2023; 14:6742. [PMID: 37875497 PMCID: PMC10597992 DOI: 10.1038/s41467-023-42425-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
It is well established that maternal thyroid hormones play an important role for the developing fetus; however, the consequences of maternal hyperthyroidism for the offspring remain poorly understood. Here we show in mice that maternal 3,3',5-triiodothyronine (T3) treatment during pregnancy leads to improved glucose tolerance in the adult male offspring and hyperactivity of brown adipose tissue (BAT) thermogenesis in both sexes starting early after birth. The activated BAT provides advantages upon cold exposure, reducing the strain on other thermogenic organs like muscle. This maternal BAT programming requires intact maternal thyroid hormone receptor β (TRβ) signaling, as offspring of mothers lacking this receptor display the opposite phenotype. On the molecular level, we identify distinct T3 induced alterations in maternal serum metabolites, including choline, a key metabolite for healthy pregnancy. Taken together, our results connect maternal TRβ activation to the fetal programming of a thermoregulatory phenotype in the offspring.
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Affiliation(s)
- Rebecca Oelkrug
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Lisbeth Harder
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mehdi Pedaran
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Straße 27, 04103, Leipzig, Germany
| | - Beke Kolms
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Julica Inderhees
- Bioanalytic Core Facility - Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Sogol Gachkar
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Julia Resch
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Kornelia Johann
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Olaf Jöhren
- Bioanalytic Core Facility - Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Kerstin Krause
- Department of Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Jens Mittag
- Institute for Endocrinology & Diabetes - Molecular Endocrinology, Center of Brain Behavior and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
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6
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Bourceau P, Geier B, Suerdieck V, Bien T, Soltwisch J, Dreisewerd K, Liebeke M. Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling. Nat Protoc 2023; 18:3050-3079. [PMID: 37674095 DOI: 10.1038/s41596-023-00864-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/31/2023] [Indexed: 09/08/2023]
Abstract
Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.
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Affiliation(s)
- Patric Bourceau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tanja Bien
- Institute of Hygiene, University of Münster, Münster, Germany
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Institute of Human Nutrition and Food Sciences, University of Kiel, Kiel, Germany.
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7
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Filipović D, Inderhees J, Korda A, Tadić P, Schwaninger M, Inta D, Borgwardt S. Metabolic Fingerprints of Effective Fluoxetine Treatment in the Prefrontal Cortex of Chronically Socially Isolated Rats: Marker Candidates and Predictive Metabolites. Int J Mol Sci 2023; 24:10957. [PMID: 37446133 PMCID: PMC10341512 DOI: 10.3390/ijms241310957] [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: 05/25/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
The increasing prevalence of depression requires more effective therapy and the understanding of antidepressants' mode of action. We carried out untargeted metabolomics of the prefrontal cortex of rats exposed to chronic social isolation (CSIS), a rat model of depression, and/or fluoxetine treatment using liquid chromatography-high resolution mass spectrometry. The behavioral phenotype was assessed by the forced swim test. To analyze the metabolomics data, we employed univariate and multivariate analysis and biomarker capacity assessment using the receiver operating characteristic (ROC) curve. We also identified the most predictive biomarkers using a support vector machine with linear kernel (SVM-LK). Upregulated myo-inositol following CSIS may represent a potential marker of depressive phenotype. Effective fluoxetine treatment reversed depressive-like behavior and increased sedoheptulose 7-phosphate, hypotaurine, and acetyl-L-carnitine contents, which were identified as marker candidates for fluoxetine efficacy. ROC analysis revealed 4 significant marker candidates for CSIS group discrimination, and 10 for fluoxetine efficacy. SVM-LK with accuracies of 61.50% or 93.30% identified a panel of 7 or 25 predictive metabolites for depressive-like behavior or fluoxetine effectiveness, respectively. Overall, metabolic fingerprints combined with the ROC curve and SVM-LK may represent a new approach to identifying marker candidates or predictive metabolites for ongoing disease or disease risk and treatment outcome.
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Affiliation(s)
- Dragana Filipović
- Department of Molecular Biology and Endocrinology, “VINČA” Institute of Nuclear Sciences—National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Julica Inderhees
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, 23562 Lübeck, Germany; (J.I.); (M.S.)
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg-Kiel-Lübeck, 20251 Hamburg, Germany
- Center of Brain Behavior and Metabolism, University of Lübeck, 23562 Lübeck, Germany
| | - Alexandra Korda
- Department of Psychiatry and Psychotherapy, Center of Brain Behavior and Metabolism, University of Lübeck, 23562 Lübeck, Germany;
| | - Predrag Tadić
- School of Electrical Engineering, University of Belgrade, 11000 Belgrade, Serbia;
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, 23562 Lübeck, Germany; (J.I.); (M.S.)
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg-Kiel-Lübeck, 20251 Hamburg, Germany
| | - Dragoš Inta
- Department for Community Health, Faculty of Natural Sciences, Medicine, University of Fribourg, 1700 Fribourg, Switzerland; (D.I.); (S.B.)
- Department of Biomedicine, University of Basel, 4001 Basel, Switzerland
| | - Stefan Borgwardt
- Department for Community Health, Faculty of Natural Sciences, Medicine, University of Fribourg, 1700 Fribourg, Switzerland; (D.I.); (S.B.)
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8
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Bhosle A, Wang Y, Franzosa EA, Huttenhower C. Progress and opportunities in microbial community metabolomics. Curr Opin Microbiol 2022; 70:102195. [PMID: 36063685 DOI: 10.1016/j.mib.2022.102195] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 01/25/2023]
Abstract
The metabolome lies at the interface of host-microbiome crosstalk. Previous work has established links between chemically diverse microbial metabolites and a myriad of host physiological processes and diseases. Coupled with scalable and cost-effective technologies, metabolomics is thus gaining popularity as a tool for characterization of microbial communities, particularly when combined with metagenomics as a window into microbiome function. A systematic interrogation of microbial community metabolomes can uncover key microbial compounds, metabolic capabilities of the microbiome, and also provide critical mechanistic insights into microbiome-linked host phenotypes. In this review, we discuss methods and accompanying resources that have been developed for these purposes. The accomplishments of these methods demonstrate that metabolomes can be used to functionally characterize microbial communities, and that microbial properties can be used to identify and investigate chemical compounds.
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Affiliation(s)
- Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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9
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Tian Z, Liu F, Li D, Fernie AR, Chen W. Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples. Comput Struct Biotechnol J 2022; 20:5085-5097. [PMID: 36187931 PMCID: PMC9489805 DOI: 10.1016/j.csbj.2022.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022] Open
Abstract
LC–MS/MS is a major analytical platform for metabolomics, which has become a recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation of small molecules based on LC–MS/MS data remains a major challenge in the chemical and biological interpretation of untargeted metabolomics datasets. In recent years, several strategies for structure elucidation using LC–MS/MS data from complex biological samples have been proposed, these strategies can be simply categorized into two types, one based on structure annotation of mass spectra and for the other on retention time prediction. These strategies have helped many scientists conduct research in metabolite-related fields and are indispensable for the development of future tools. Here, we summarized the characteristics of the current tools and strategies for structure elucidation of small molecules based on LC–MS/MS data, and further discussed the directions and perspectives to improve the power of the tools or strategies for structure elucidation.
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Pandohee J, Kyereh E, Kulshrestha S, Xu B, Mahomoodally MF. Review of the recent developments in metabolomics-based phytochemical research. Crit Rev Food Sci Nutr 2021:1-16. [PMID: 34672234 DOI: 10.1080/10408398.2021.1993127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phytochemicals are important bioactive components present in natural products. Although the health benefits of many food products are well-known and accepted as a common knowledge, the identity of the main bioactive molecules and the mechanism by which they interact in the body of human are often unknown. It was only in the last 30 years when the field of metabolomics had matured that the identification of such molecules with bioactivity has been made possible through the development of instruments to separate and computational techniques to characterize complex samples. This in turn has enabled in vitro studies to quantify the biological activity of the respective phytochemical either in mice models or in humans. In this review, the importance of key dietary phytochemicals such as phenolic acids, flavonoids, carotenoids, resveratrol, curcumin, and capsaicinoids are discussed together with their potential functions for human health. Untargeted metabolomics, in particular, liquid chromatography mass spectrometry, is the most used method to isolate, identify and profile bioactive compounds in the study of phytochemicals in foods. The application of metabolomics in drug discovery is a common practice nowadays and has boosted the drug and/or supplement manufacturing sector.HighlightsPhytochemicals are beneficial compounds for human healthPhytochemicals are plant-based bioactive and obtainable from natural productsUntargeted metabolomics has boosted the discovery of phytochemicals from foodTargeted metabolomics is key in the authentication and screening of phytochemicalsMetabolomics of phytochemicals is reshaping the road to drug and supplement manufacture.
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Affiliation(s)
- Jessica Pandohee
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia.,Department of Health Sciences, Faculty of Science, University of Mauritius, Réduit, Mauritius
| | | | - Saurabh Kulshrestha
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Baojun Xu
- Food Science and Technology Program, BNU-HKBU United International College, Zhuhai, Guangdong, China
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11
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Lavarello C, Barco S, Bartolucci M, Panfoli I, Magi E, Tripodi G, Petretto A, Cangemi G. Development of an Accurate Mass Retention Time Database for Untargeted Metabolomic Analysis and Its Application to Plasma and Urine Pediatric Samples. Molecules 2021; 26:molecules26144256. [PMID: 34299531 PMCID: PMC8303579 DOI: 10.3390/molecules26144256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 07/09/2021] [Indexed: 01/17/2023] Open
Abstract
Liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is currently the method of choice for untargeted metabolomic analysis. The availability of established protocols to achieve a high confidence identification of metabolites is crucial. The aim of this work is to describe the workflow that we have applied to build an Accurate Mass Retention Time (AMRT) database using a commercial metabolite library of standards. LC-HRMS analysis was carried out using a Vanquish Horizon UHPLC system coupled to a Q-Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Milan, Italy). The fragmentation spectra, obtained with 12 collision energies, were acquired for each metabolite, in both polarities, through flow injection analysis. Several chromatographic conditions were tested to obtain a protocol that yielded stable retention times. The adopted chromatographic protocol included a gradient separation using a reversed phase (Waters Acquity BEH C18) and a HILIC (Waters Acquity BEH Amide) column. An AMRT database of 518 compounds was obtained and tested on real plasma and urine samples analyzed in data-dependent acquisition mode. Our AMRT library allowed a level 1 identification, according to the Metabolomics Standards Initiative, of 132 and 124 metabolites in human pediatric plasma and urine samples, respectively. This library represents a starting point for future metabolomic studies in pediatric settings.
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Affiliation(s)
- Chiara Lavarello
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (C.L.); (M.B.)
- Department of Chemistry and Industrial Chemistry, University of Genoa, 16146 Genoa, Italy;
| | - Sebastiano Barco
- Chromatography and Mass Spectrometry Section, Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.B.); (G.T.); (G.C.)
| | - Martina Bartolucci
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (C.L.); (M.B.)
| | - Isabella Panfoli
- DIFAR-Biochemistry Laboratory, University of Genoa, 16132 Genova, Italy;
| | - Emanuele Magi
- Department of Chemistry and Industrial Chemistry, University of Genoa, 16146 Genoa, Italy;
| | - Gino Tripodi
- Chromatography and Mass Spectrometry Section, Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.B.); (G.T.); (G.C.)
| | - Andrea Petretto
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (C.L.); (M.B.)
- Correspondence: ; Tel.: +39-01056362911
| | - Giuliana Cangemi
- Chromatography and Mass Spectrometry Section, Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.B.); (G.T.); (G.C.)
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12
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Dvorak Z, Klapholz M, Burris TP, Willing BP, Gioiello A, Pellicciari R, Galli F, March J, O'Keefe SJ, Sartor RB, Kim CH, Levy M, Mani S. Weak Microbial Metabolites: a Treasure Trove for Using Biomimicry to Discover and Optimize Drugs. Mol Pharmacol 2020; 98:343-349. [PMID: 32764096 PMCID: PMC7485585 DOI: 10.1124/molpharm.120.000035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
For decades, traditional drug discovery has used natural product and synthetic chemistry approaches to generate libraries of compounds, with some ending as promising drug candidates. A complementary approach has been to adopt the concept of biomimicry of natural products and metabolites so as to improve multiple drug-like features of the parent molecule. In this effort, promiscuous and weak interactions between ligands and receptors are often ignored in a drug discovery process. In this Emerging Concepts article, we highlight microbial metabolite mimicry, whereby parent metabolites have weak interactions with their receptors that then have led to discrete examples of more potent and effective drug-like molecules. We show specific examples of parent-metabolite mimics with potent effects in vitro and in vivo. Furthermore, we show examples of emerging microbial ligand-receptor interactions and provide a context in which these ligands could be improved as potential drugs. A balanced conceptual advance is provided in which we also acknowledge potential pitfalls-hyperstimulation of finely balanced receptor-ligand interactions could also be detrimental. However, with balance, we provide examples of where this emerging concept needs to be tested. SIGNIFICANCE STATEMENT: Microbial metabolite mimicry is a novel way to expand on the chemical repertoire of future drugs. The emerging concept is now explained using specific examples of the discovery of therapeutic leads from microbial metabolites.
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Affiliation(s)
- Zdenek Dvorak
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Max Klapholz
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Thomas P Burris
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Benjamin P Willing
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Antimo Gioiello
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Roberto Pellicciari
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Francesco Galli
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - John March
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Stephen J O'Keefe
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - R Balfour Sartor
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Chang H Kim
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Maayan Levy
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
| | - Sridhar Mani
- Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic (Z.D.); Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania (M.K., M.L.); The Center for Clinical Pharmacology, Washington University in St. Louis and St. Louis College of Pharmacy, St. Louis, Missouri (T.P.B.); Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta (B.P.W.); Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy (A.G., F.G.); TES Pharma, Corso Vannucci, Perugia, Italy (R.P.); The Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York (J.M.); Division of Gastroenterology and Nutrition, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania (S.J.O.); Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (R.B.S.); Department of Pathology, Mary H. Weiser Food Allergy Center, and Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.); and Department of Medicine, Albert Einstein College of Medicine, Bronx, New York (S.M.)
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