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Article ; Online: Primary Human M2 Macrophage Subtypes Are Distinguishable by Aqueous Metabolite Profiles.

Fuchs, Amanda L / Costello, Stephanann M / Schiller, Sage M / Tripet, Brian P / Copié, Valérie

International journal of molecular sciences

2024 Volume 25, Issue 4

Abstract: The complexity of macrophage (MΦ) plasticity and polarization states, which include classically activated pro-inflammatory (M1) and alternatively activated anti-inflammatory (M2) MΦ phenotypes, is becoming increasingly appreciated. Within the M2 MΦ ... ...

Abstract	The complexity of macrophage (MΦ) plasticity and polarization states, which include classically activated pro-inflammatory (M1) and alternatively activated anti-inflammatory (M2) MΦ phenotypes, is becoming increasingly appreciated. Within the M2 MΦ polarization state, M2a, M2b, M2c, and M2d MΦ subcategories have been defined based on their expression of specific cell surface receptors, secreted cytokines, and specialized immune effector functions. The importance of immunometabolic networks in mediating the function and regulation of MΦ immune responses is also being increasingly recognized, although the exact mechanisms and extent of metabolic modulation of MΦ subtype phenotypes and functions remain incompletely understood. In this study, proton (
MeSH term(s)	Humans ; Macrophages/metabolism ; Cytokines/metabolism ; Phenotype ; Receptors, Cell Surface/metabolism ; Macrophage Activation ; Cell Differentiation
Chemical Substances	Cytokines ; Receptors, Cell Surface
Language	English
Publishing date	2024-02-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25042407
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Article ; Online: Correction for Meslé et al., "Isolation and Characterization of Lignocellulose-Degrading Geobacillus thermoleovorans from Yellowstone National Park".

Meslé, Margaux M / Mueller, Rebecca C / Peach, Jesse / Eilers, Brian / Tripet, Brian P / Bothner, Brian / Copié, Valérie / Peyton, Brent M

Applied and environmental microbiology

2022 Volume 88, Issue 9, Page(s) e0059822

Language	English
Publishing date	2022-04-19
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.00598-22
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Article ; Online: Metabolomic profiling of human bladder tissue extracts.

Ossoliński, Krzysztof / Ruman, Tomasz / Copié, Valérie / Tripet, Brian P / Kołodziej, Artur / Płaza-Altamer, Aneta / Ossolińska, Anna / Ossoliński, Tadeusz / Krupa, Zuzanna / Nizioł, Joanna

Metabolomics : Official journal of the Metabolomic Society

2024 Volume 20, Issue 1, Page(s) 14

Abstract: Introduction: Bladder cancer is a common malignancy affecting the urinary tract and effective biomarkers and for which monitoring therapeutic interventions have yet to be identified.: Objectives: Major aim of this work was to perform metabolomic ... ...

Abstract	Introduction: Bladder cancer is a common malignancy affecting the urinary tract and effective biomarkers and for which monitoring therapeutic interventions have yet to be identified. Objectives: Major aim of this work was to perform metabolomic profiling of human bladder cancer and adjacent normal tissue and to evaluate cancer biomarkers. Methods: This study utilized nuclear magnetic resonance (NMR) and high-resolution nanoparticle-based laser desorption/ionization mass spectrometry (LDI-MS) methods to investigate polar metabolite profiles in tissue samples from 99 bladder cancer patients. Results: Through NMR spectroscopy, six tissue metabolites were identified and quantified as potential indicators of bladder cancer, while LDI-MS allowed detection of 34 compounds which distinguished cancer tissue samples from adjacent normal tissue. Thirteen characteristic tissue metabolites were also found to differentiate bladder cancer tumor grades and thirteen metabolites were correlated with tumor stages. Receiver-operating characteristics analysis showed high predictive power for all three types of metabolomics data, with area under the curve (AUC) values greater than 0.853. Conclusion: To date, this is the first study in which bladder human normal tissues adjacent to cancerous tissues are analyzed using both NMR and MS method. These findings suggest that the metabolite markers identified in this study may be useful for the detection and monitoring of bladder cancer stages and grades.
MeSH term(s)	Humans ; Urinary Bladder ; Metabolomics ; Urinary Bladder Neoplasms ; Area Under Curve ; Biomarkers, Tumor
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2250617-2
ISSN	1573-3890 ; 1573-3882
ISSN (online)	1573-3890
ISSN	1573-3882
DOI	10.1007/s11306-023-02076-w
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Article ; Online: Isolation and Characterization of Lignocellulose-Degrading

Meslé, Margaux M / Mueller, Rebecca C / Peach, Jesse / Eilers, Brian / Tripet, Brian P / Bothner, Brian / Copié, Valérie / Peyton, Brent M

Applied and environmental microbiology

2021 Volume 88, Issue 1, Page(s) e0095821

Abstract: The microbial degradation of lignocellulose in natural ecosystems presents numerous biotechnological opportunities, including biofuel production from agricultural waste and feedstock biomass. To explore the degradation potential of specific thermophiles, ...

Abstract	The microbial degradation of lignocellulose in natural ecosystems presents numerous biotechnological opportunities, including biofuel production from agricultural waste and feedstock biomass. To explore the degradation potential of specific thermophiles, we have identified and characterized extremophilic microorganisms isolated from hot springs environments that are capable of biodegrading lignin and cellulose substrates under thermoalkaline conditions, using a combination of culturing, genomics, and metabolomics techniques. Organisms that can use lignin and cellulose as a sole carbon source at 60 to 75°C were isolated from sediment slurry of thermoalkaline hot springs (71 to 81°C and pH 8 to 9) of Yellowstone National Park. Full-length 16S rRNA gene sequencing indicated that these isolates were closely related to Geobacillus thermoleovorans. Interestingly, most of these isolates demonstrated biofilm formation on lignin, a phenotype that is correlated with increased bioconversion. Assessment of metabolite level changes in two
MeSH term(s)	Biomass ; Ecosystem ; Geobacillus/genetics ; Lignin ; Parks, Recreational ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S ; lignocellulose (11132-73-3) ; Lignin (9005-53-2)
Language	English
Publishing date	2021-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.00958-21
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Article ; Online: Distinct Metabolic States Are Observed in Hypoglycemia Induced in Mice by Ricin Toxin or by Fasting.

Kempa, Jacob / O'Shea-Stone, Galen / Moss, Corinne E / Peters, Tami / Marcotte, Tamera K / Tripet, Brian / Eilers, Brian / Bothner, Brian / Copié, Valérie / Pincus, Seth H

Toxins

2022 Volume 14, Issue 12

Abstract: Hypoglycemia may be induced by a variety of physiologic and pathologic stimuli and can result in life-threatening consequences if untreated. However, hypoglycemia may also play a role in the purported health benefits of intermittent fasting and caloric ... ...

Abstract	Hypoglycemia may be induced by a variety of physiologic and pathologic stimuli and can result in life-threatening consequences if untreated. However, hypoglycemia may also play a role in the purported health benefits of intermittent fasting and caloric restriction. Previously, we demonstrated that systemic administration of ricin toxin induced fatal hypoglycemia in mice. Here, we examine the metabolic landscape of the hypoglycemic state induced in the liver of mice by two different stimuli: systemic ricin administration and fasting. Each stimulus produced the same decrease in blood glucose and weight loss. The polar metabolome was studied using
MeSH term(s)	Animals ; Mice ; Blood Glucose ; Fasting/adverse effects ; Hypoglycemia/chemically induced ; Hypoglycemia/etiology ; Hypoglycemia/metabolism ; Metabolome ; Metabolomics/methods ; Ricin/toxicity
Chemical Substances	Blood Glucose ; Ricin (9009-86-3)
Language	English
Publishing date	2022-11-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2518395-3
ISSN	2072-6651 ; 2072-6651
ISSN (online)	2072-6651
ISSN	2072-6651
DOI	10.3390/toxins14120815
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Article: A Comprehensive NMR Analysis of Serum and Fecal Metabolites in Familial Dysautonomia Patients Reveals Significant Metabolic Perturbations.

Costello, Stephanann M / Cheney, Alexandra M / Waldum, Annie / Tripet, Brian / Cotrina-Vidal, Maria / Kaufmann, Horacio / Norcliffe-Kaufmann, Lucy / Lefcort, Frances / Copié, Valérie

Metabolites

2023 Volume 13, Issue 3

Abstract: Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer's (AD) and Parkinson's (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the ...

Abstract	Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer's (AD) and Parkinson's (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the multifactorial origin of these neurological diseases, neurodevelopmental impairment and neurodegeneration in Familial Dysautonomia (FD) results from a single point mutation in the
Language	English
Publishing date	2023-03-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo13030433
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Article ; Online: Gut microbiome dysbiosis drives metabolic dysfunction in Familial dysautonomia.

Cheney, Alexandra M / Costello, Stephanann M / Pinkham, Nicholas V / Waldum, Annie / Broadaway, Susan C / Cotrina-Vidal, Maria / Mergy, Marc / Tripet, Brian / Kominsky, Douglas J / Grifka-Walk, Heather M / Kaufmann, Horacio / Norcliffe-Kaufmann, Lucy / Peach, Jesse T / Bothner, Brian / Lefcort, Frances / Copié, Valérie / Walk, Seth T

Nature communications

2023 Volume 14, Issue 1, Page(s) 218

Abstract: Familial dysautonomia (FD) is a rare genetic neurologic disorder caused by impaired neuronal development and progressive degeneration of both the peripheral and central nervous systems. FD is monogenic, with >99.4% of patients sharing an identical point ... ...

Abstract	Familial dysautonomia (FD) is a rare genetic neurologic disorder caused by impaired neuronal development and progressive degeneration of both the peripheral and central nervous systems. FD is monogenic, with >99.4% of patients sharing an identical point mutation in the elongator acetyltransferase complex subunit 1 (ELP1) gene, providing a relatively simple genetic background in which to identify modifiable factors that influence pathology. Gastrointestinal symptoms and metabolic deficits are common among FD patients, which supports the hypothesis that the gut microbiome and metabolome are altered and dysfunctional compared to healthy individuals. Here we show significant differences in gut microbiome composition (16 S rRNA gene sequencing of stool samples) and NMR-based stool and serum metabolomes between a cohort of FD patients (~14% of patients worldwide) and their cohabitating, healthy relatives. We show that key observations in human subjects are recapitulated in a neuron-specific Elp1-deficient mouse model, and that cohousing mutant and littermate control mice ameliorates gut microbiome dysbiosis, improves deficits in gut transit, and reduces disease severity. Our results provide evidence that neurologic deficits in FD alter the structure and function of the gut microbiome, which shifts overall host metabolism to perpetuate further neurodegeneration.
MeSH term(s)	Humans ; Mice ; Animals ; Dysautonomia, Familial/genetics ; Gastrointestinal Microbiome ; Dysbiosis/metabolism ; Neurons/metabolism ; Central Nervous System/metabolism
Language	English
Publishing date	2023-01-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-35787-8
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Article ; Online: Nuclear magnetic resonance and surface-assisted laser desorption/ionization mass spectrometry-based serum metabolomics of kidney cancer.

Nizioł, Joanna / Ossoliński, Krzysztof / Tripet, Brian P / Copié, Valérie / Arendowski, Adrian / Ruman, Tomasz

Analytical and bioanalytical chemistry

2020 Volume 412, Issue 23, Page(s) 5827–5841

Abstract: Kidney cancer is one of the most frequently diagnosed and the most lethal urinary cancer. Despite all the efforts made, no serum-specific biomarker is currently used in the clinical management of patients with this tumor. In this study, comprehensive ... ...

Abstract	Kidney cancer is one of the most frequently diagnosed and the most lethal urinary cancer. Despite all the efforts made, no serum-specific biomarker is currently used in the clinical management of patients with this tumor. In this study, comprehensive high-resolution proton nuclear magnetic resonance spectroscopy (
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor/blood ; Case-Control Studies ; Female ; Humans ; Kidney Neoplasms/blood ; Magnetic Resonance Spectroscopy/methods ; Male ; Mass Spectrometry/methods ; Metabolomics/methods ; Middle Aged
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2020-07-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-020-02807-1
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Article ; Online: Targeted and untargeted urinary metabolic profiling of bladder cancer.

Ossoliński, Krzysztof / Ruman, Tomasz / Copié, Valérie / Tripet, Brian P / Kołodziej, Artur / Płaza-Altamer, Aneta / Ossolińska, Anna / Ossoliński, Tadeusz / Nieczaj, Anna / Nizioł, Joanna

Journal of pharmaceutical and biomedical analysis

2023 Volume 233, Page(s) 115473

Abstract: Bladder cancer (BC) is frequent cancer affecting the urinary tract and is one of the most prevalent malignancies worldwide. No biomarkers that can be used for effective monitoring of therapeutic interventions for this cancer have been identified to date. ...

Abstract	Bladder cancer (BC) is frequent cancer affecting the urinary tract and is one of the most prevalent malignancies worldwide. No biomarkers that can be used for effective monitoring of therapeutic interventions for this cancer have been identified to date. This study investigated polar metabolite profiles in urine samples from 100 BC patients and 100 normal controls (NCs) using nuclear magnetic resonance (NMR) and two methods of high-resolution nanoparticle-based laser desorption/ionization mass spectrometry (LDI-MS). Five urine metabolites were identified and quantified using NMR spectroscopy to be potential indicators of bladder cancer. Twenty-five LDI-MS-detected compounds, predominantly peptides and lipids, distinguished urine samples from BC and NCs individuals. Level changes of three characteristic urine metabolites enabled BC tumor grades to be distinguished, and ten metabolites were reported to correlate with tumor stages. Receiver-Operating Characteristics analysis showed high predictive power for all three types of metabolomics data, with the area under the curve (AUC) values greater than 0.87. These findings suggest that metabolite markers identified in this study may be useful for the non-invasive detection and monitoring of bladder cancer stages and grades.
MeSH term(s)	Humans ; Biomarkers, Tumor/urine ; Urinary Bladder Neoplasms/diagnosis ; Metabolomics/methods ; Mass Spectrometry/methods ; Urinary Tract/metabolism
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2023-05-22
Publishing country	England
Document type	Journal Article
ZDB-ID	604917-5
ISSN	1873-264X ; 0731-7085
ISSN (online)	1873-264X
ISSN	0731-7085
DOI	10.1016/j.jpba.2023.115473
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Article ; Online: Nuclear magnetic resonance and surface-assisted laser desorption/ionization mass spectrometry-based metabolome profiling of urine samples from kidney cancer patients.

Nizioł, Joanna / Ossoliński, Krzysztof / Tripet, Brian P / Copié, Valérie / Arendowski, Adrian / Ruman, Tomasz

Journal of pharmaceutical and biomedical analysis

2020 Volume 193, Page(s) 113752

Abstract: Kidney cancer is one of the most frequently diagnosed cancers of the urinary tract in the world. Despite significant advances in kidney cancer treatment, no urine specific biomarker is currently used to guide therapeutic interventions. In an effort to ... ...

Abstract	Kidney cancer is one of the most frequently diagnosed cancers of the urinary tract in the world. Despite significant advances in kidney cancer treatment, no urine specific biomarker is currently used to guide therapeutic interventions. In an effort to address this knowledge gap, metabolic profiling of urine samples from 50 patients with kidney cancer and 50 healthy volunteers was undertaken using high-resolution proton nuclear magnetic resonance spectroscopy (
MeSH term(s)	Humans ; Kidney Neoplasms ; Lasers ; Magnetic Resonance Spectroscopy ; Metabolome ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Language	English
Publishing date	2020-11-06
Publishing country	England
Document type	Journal Article
ZDB-ID	604917-5
ISSN	1873-264X ; 0731-7085
ISSN (online)	1873-264X
ISSN	0731-7085
DOI	10.1016/j.jpba.2020.113752
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