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Tao Y, Zhao Q, Liu F, Liang X, Li Q. Enzymes encapsulated in organic-inorganic hybrid nanoflower with spatial localization for sensitive and colorimetric detection of formate. J Colloid Interface Sci 2024; 672:97-106. [PMID: 38833738 DOI: 10.1016/j.jcis.2024.05.231] [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: 02/29/2024] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
Formate is an important environmental pollutant, and meanwhile its concentration change is associated with a variety of diseases. Thus, rapid and sensitive detection of formate is critical for the biochemical analysis of complex samples and clinical diagnosis of multiple diseases. Herein, a colorimetric biosensor was constructed based on the cascade catalysis of formate oxidase (FOx) and horseradish peroxidase (HRP). These two enzymes were co-immobilized in Cu3(PO4)2-based hybrid nanoflower with spatial localization, in which FOx and HRP were located in the shell and core of nanoflower, respectively (FOx@HRP). In this system, FOx could catalyze the oxidation of formate to generate H2O2, which was then utilized by HRP to oxidize 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid to yield blue product. Ideal linear correlation could be obtained between the absorbance at 420 nm and formate concentration. Meanwhile, FOx@HRP exhibited excellent detection performance with low limit of detection (6 μM), wide linear detection range (10-900 μM), and favorable specificity, stability and reusability. Moreover, it could be applied in the detection of formate in environmental, food and biological samples with high accuracy. Collectively, FOx@HRP provides a useful strategy for the simple and sensitive detection of formate and is potentially to be used in biochemical analysis and clinical diagnosis.
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Affiliation(s)
- Yu Tao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Qixuan Zhao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Fengmei Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xiao Liang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Quanshun Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; Center for Supramolecular Chemical Biology, Jilin University, Changchun 130012, China.
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Giovanini de Oliveira Sartori A, Silva Antonelo D, Ribeiro GH, Colnago LA, de Carvalho Balieiro JC, Francisquine Delgado E, Contreras Castillo CJ. Lipidome and metabolome profiling of longissimus lumborum beef with different ultimate pH and postmortem aging. Meat Sci 2024; 217:109621. [PMID: 39116534 DOI: 10.1016/j.meatsci.2024.109621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/15/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
The objective of this exploratory study was to assess the changes on lipidome and metabolome profiling of Longissimus lumborum bull muscle with different ultimate pH (pHu) and aging periods. The bull muscles classified as normal, intermediate, or high pHu were collected from a Brazilian commercial slaughterhouse, cut into steaks, individually vacuum-packaged, and aged for 3 days (3-d) or 21 days (21-d) at 2 °C. Muscle extracts were analyzed for the profiles of both lipids, by mass spectrometry (via direct flow-injection), and metabolites, by nuclear magnetic resonance, with downstream multivariate data analysis. As major results, pairwise comparisons identified C12:0 and C14:0 acylcarnitines as potential biomarkers of the intermediate pHu-muscle, which are related to lipid catabolism for alternative energy metabolism and indicate less protein breakage postmortem. Interestingly, the concentration of arginine at early postmortem aging (3-d) may influence the previously reported improved tenderness in normal and high pHu-muscles. Moreover, upregulation of fumarate, formate, and acetate with increased pHu muscle at 21-d aging indicate more intense tricarboxylic acid cycle, amino acid degradation, and pyruvate oxidation by reactive oxygen species, respectively. These three compounds (fumarate, formate, and acetate) discriminated statistically the muscle with high pHu at 21-d aging. The normal pHu-muscle showed higher concentrations of glycogenolysis and glycolysis metabolites, including glucose, mannose, and pyruvate. Hence, our results enhance knowledge of postmortem biochemical changes of beef within different pHu groups aged up to 21 days, which is essential to understand the mechanisms underpinning bull meat quality changes.
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Kulecka M, Czarnowski P, Bałabas A, Turkot M, Kruczkowska-Tarantowicz K, Żeber-Lubecka N, Dąbrowska M, Paszkiewicz-Kozik E, Walewski J, Ługowska I, Koseła-Paterczyk H, Rutkowski P, Kluska A, Piątkowska M, Jagiełło-Gruszfeld A, Tenderenda M, Gawiński C, Wyrwicz L, Borucka M, Krzakowski M, Zając L, Kamiński M, Mikula M, Ostrowski J. Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients. Int J Mol Sci 2024; 25:8026. [PMID: 39125593 PMCID: PMC11311272 DOI: 10.3390/ijms25158026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Paweł Czarnowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maryla Turkot
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Kamila Kruczkowska-Tarantowicz
- Department of Internal Medicine and Hematology, Military Institute of Medicine—National Research Institute, 04-141 Warsaw, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Ewa Paszkiewicz-Kozik
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Iwona Ługowska
- Early Phase Clinical Trials Unit, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Hanna Koseła-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Agnieszka Jagiełło-Gruszfeld
- Department of Breast Cancer & Reconstructive Surgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Tenderenda
- Department of Oncological Surgery and Neuroendocrine Tumors, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Cieszymierz Gawiński
- Department of Oncology and Radiotherapy, Maria Sklodowska-Curie National Cancer Research Institute, 02-781 Warsaw, Poland
| | - Lucjan Wyrwicz
- Department of Oncology and Radiotherapy, Maria Sklodowska-Curie National Cancer Research Institute, 02-781 Warsaw, Poland
| | - Magdalena Borucka
- Department of Lung and Chest Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maciej Krzakowski
- Department of Lung and Chest Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Leszek Zając
- Department of Gastrointestinal Surgical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Kamiński
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
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García-Poyatos C, Arora P, Calvo E, Marques IJ, Kirschke N, Galardi-Castilla M, Lembke C, Meer M, Fernández-Montes P, Ernst A, Haberthür D, Hlushchuk R, Vázquez J, Vermathen P, Enríquez JA, Mercader N. Cox7a1 controls skeletal muscle physiology and heart regeneration through complex IV dimerization. Dev Cell 2024; 59:1824-1841.e10. [PMID: 38701784 DOI: 10.1016/j.devcel.2024.04.012] [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: 07/28/2023] [Revised: 01/30/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024]
Abstract
The oxidative phosphorylation (OXPHOS) system is intricately organized, with respiratory complexes forming super-assembled quaternary structures whose assembly mechanisms and physiological roles remain under investigation. Cox7a2l, also known as Scaf1, facilitates complex III and complex IV (CIII-CIV) super-assembly, enhancing energetic efficiency in various species. We examined the role of Cox7a1, another Cox7a family member, in supercomplex assembly and muscle physiology. Zebrafish lacking Cox7a1 exhibited reduced CIV2 formation, metabolic alterations, and non-pathological muscle performance decline. Additionally, cox7a1-/- hearts displayed a pro-regenerative metabolic profile, impacting cardiac regenerative response. The distinct phenotypic effects of cox7a1-/- and cox7a2l-/- underscore the diverse metabolic and physiological consequences of impaired supercomplex formation, emphasizing the significance of Cox7a1 in muscle maturation within the OXPHOS system.
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Affiliation(s)
- Carolina García-Poyatos
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Centro de Investigación Biomédica en red en Fragilidad y Envejecimiento saludable (CIBERFES), Madrid, Spain
| | - Prateek Arora
- Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland; Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Centro de Investigación Biomédica en red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ines J Marques
- Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland; Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland
| | - Nick Kirschke
- Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland; Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland
| | | | - Carla Lembke
- Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland; Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland
| | - Marco Meer
- Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland; Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland
| | | | - Alexander Ernst
- Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland
| | - David Haberthür
- MicroCT research group, Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Ruslan Hlushchuk
- MicroCT research group, Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Centro de Investigación Biomédica en red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Peter Vermathen
- University Institute of Diagnostic and Interventional Neuroradiology, Magnetic Resonance Methodology, University of Bern, Bern, Switzerland
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Centro de Investigación Biomédica en red en Fragilidad y Envejecimiento saludable (CIBERFES), Madrid, Spain.
| | - Nadia Mercader
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Department of Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland; Department for Biomedical Research, Cardiovascular Disease Program, University of Bern, Bern, Switzerland.
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5
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Soares RB, Pinto J, Amaro F, Manguinhas R, Gil N, Rosell R, Batinic-Haberle I, Fernandes AS, Oliveira NG, Guedes de Pinho P. Impact of the redox-active MnTnHex-2-PyP 5+ and cisplatin on the metabolome of non-small cell lung cancer cells. Biochem Pharmacol 2024; 227:116424. [PMID: 39004232 DOI: 10.1016/j.bcp.2024.116424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/07/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]
Abstract
Redox-based cancer therapeutic strategies aim to raise reactive oxygen species (ROS) levels in cancer cells, thus modifying their redox status, and eventually inducing cell death. Promising compounds, known as superoxide dismutase mimics (SODm), e.g. MnTnHex-2-Py5+ (MnTnHex), could increase intracellular H2O2 in cancer cells with deficient ROS removal systems and therefore enhance radio- and chemotherapy efficacy. We have previously shown that MnTnHex was cytotoxic either alone or combined with cisplatin to non-small cell lung cancer (NSCLC) cells. To gain a deeper understanding of the effects and safety of this compound, it is crucial to analyze the metabolic alterations that take place within the cell. Our goal was thus to study the intracellular metabolome (intracellular metabolites) of NSCLC cells (A549 and H1975) using nuclear magnetic resonance (NMR) spectroscopy-based metabolomics to evaluate the changes in cellular metabolism upon exposure to MnTnHex per se or in combination with cisplatin. 1H NMR metabolomics revealed a higher number of significantly altered metabolites in A549 cells exposed to MnTnHex alone or combined with cisplatin in comparison with non-treated cells (nine dysregulated metabolites), suggesting an impact on aminoacyl-tRNA biosynthesis, glycolysis/gluconeogenesis, taurine, hypotaurine, glycerophospholipid, pyruvate, arginine and proline metabolisms. Regarding H1975 cells, significant alterations in the levels of six metabolites were observed upon co-treatment with MnTnHex and cisplatin, suggesting dysregulations in aminoacyl-tRNA biosynthesis, arginine and proline metabolism, pyruvate metabolism, and glycolysis/gluconeogenesis. These findings help us to understand the impact of MnTnHex on NSCLC cells. Importantly, specific altered metabolites, such as taurine, may contribute to the chemosensitizing effects of MnTnHex.
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Affiliation(s)
- Rita B Soares
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal; Lung Unit, Champalimaud Clinical Centre, Champalimaud Foundation, Av. Brasília, 1400-038 Lisbon, Portugal
| | - Joana Pinto
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Filipa Amaro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Rita Manguinhas
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Nuno Gil
- Lung Unit, Champalimaud Clinical Centre, Champalimaud Foundation, Av. Brasília, 1400-038 Lisbon, Portugal
| | - Rafael Rosell
- Dr. Rosell Oncology Institute, 08028 Barcelona, Spain; Institute Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain
| | - Ines Batinic-Haberle
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ana S Fernandes
- Universidade Lusófona's Research Center for Biosciences & Health Technologies (CBIOS), Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Nuno G Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal.
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, 4050-313 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Lab. of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
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6
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Martin-Grau M, Monleón D. The Role of Microbiota-Related Co-Metabolites in MASLD Progression: A Narrative Review. Curr Issues Mol Biol 2024; 46:6377-6389. [PMID: 39057023 PMCID: PMC11276081 DOI: 10.3390/cimb46070381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) represents a growing health concern due to its increasing prevalence worldwide. Metabolic homeostasis encompasses the stable internal conditions vital for efficient metabolism. This equilibrium extends to the intestinal microbiota, whose metabolic activities profoundly influence overall metabolic balance and organ health. The metabolites derived from the gut microbiota metabolism can be defined as microbiota-related co-metabolites. They serve as mediators between the gut microbiota and the host, influencing various physiological processes. The recent redefinition of the term MASLD has highlighted the metabolic dysfunction that characterize the disease. Metabolic dysfunction encompasses a spectrum of abnormalities, including impaired glucose regulation, dyslipidemia, mitochondrial dysfunction, inflammation, and accumulation of toxic byproducts. In addition, MASLD progression has been linked to dysregulation in the gut microbiota and associated co-metabolites. Short-chain fatty acids (SCFAs), hippurate, indole derivatives, branched-chain amino acids (BCAAs), and bile acids (BAs) are among the key co-metabolites implicated in MASLD progression. In this review, we will unravel the relationship between the microbiota-related metabolites which have been associated with MASLD and that could play an important role for developing effective therapeutic interventions for MASLD and related metabolic disorders.
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Affiliation(s)
- Maria Martin-Grau
- Department of Pathology, University of Valencia, 46010 Valencia, Spain
- University Clinical Hospital of Valencia Research Foundation (INCLIVA), 46010 Valencia, Spain
| | - Daniel Monleón
- Department of Pathology, University of Valencia, 46010 Valencia, Spain
- University Clinical Hospital of Valencia Research Foundation (INCLIVA), 46010 Valencia, Spain
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7
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Osik N, Lukzen NN, Yanshole VV, Tsentalovich YP. Loss of Volatile Metabolites during Concentration of Metabolomic Extracts. ACS OMEGA 2024; 9:24015-24024. [PMID: 38854568 PMCID: PMC11154959 DOI: 10.1021/acsomega.4c02439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024]
Abstract
Volatile metabolites can be lost during the preanalytical stage of metabolomic analysis. This work is aimed at the experimental and theoretical study of mechanisms of volatile substance evaporation and retention in the residues during the drying of extract solutions. We demonstrate that solvent evaporation leads to the unavoidable loss of nondissociating volatile metabolites with low boiling points and high vapor pressures (such as acetone and ethanol). The retention of dissociating volatile compounds (primarily organic acids RH) during the evaporation depends on the presence of buffer salts in solution, which are responsible for maintaining the neutral pH. An acid remains in the solution as long as it is present predominantly in the dissociated R- state. At the very last stage of solvent evaporation, buffer salts precipitate, forming a solid matrix for metabolite trapping in the residue. At the same time, buffer precipitation leads to a decrease of the solution pH, increase of the portion of RH in associated state, and acceleration of RH volatilization. The RH recovery is thus determined by the competition between the solute volatilization in the associated RH form and metabolite trapping in the solid matrix. The retention of volatile acids in the residue after extract drying can be improved either by adding buffer salts to maintain high pH or by incomplete sample drying.
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Affiliation(s)
- Nataliya
A. Osik
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
| | - Nikita N. Lukzen
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
- Novosibirsk
State University, Pirogova
str. 1, Novosibirsk 630090, Russia
| | - Vadim V. Yanshole
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
- Novosibirsk
State University, Pirogova
str. 1, Novosibirsk 630090, Russia
| | - Yuri P. Tsentalovich
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
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8
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Chen J, Chen W, Zhang J, Zhao H, Cui J, Wu J, Shi A. Dual effects of endogenous formaldehyde on the organism and drugs for its removal. J Appl Toxicol 2024; 44:798-817. [PMID: 37766419 DOI: 10.1002/jat.4546] [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: 07/31/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Endogenous formaldehyde (FA) is produced in the human body via various mechanisms to preserve healthy energy metabolism and safeguard the organism. However, endogenous FA can have several negative effects on the body through epigenetic alterations, including cancer growth promotion; neuronal, hippocampal and endothelial damages; atherosclerosis acceleration; haemopoietic stem cell destruction and haemopoietic cell production reduction. Certain medications with antioxidant effects, such as glutathione, vitamin E, resveratrol, alpha lipoic acid and polyphenols, lessen the detrimental effects of endogenous FA by reducing oxidative stress, directly scavenging endogenous FA or promoting its degradation. This study offers fresh perspectives for managing illnesses associated with endogenous FA exposure.
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Affiliation(s)
- Jiaxin Chen
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Wenhui Chen
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Jinjia Zhang
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Huanhuan Zhao
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Ji Cui
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Junzi Wu
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
- Department of Basic Medical, Yunnan University of Chinese Medicine, Kunming, China
| | - Anhua Shi
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
- Department of Basic Medical, Yunnan University of Chinese Medicine, Kunming, China
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9
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Fotakis C, Amanatidou AI, Kafyra M, Andreou V, Kalafati IP, Zervou M, Dedoussis GV. Circulatory Metabolite Ratios as Indicators of Lifestyle Risk Factors Based on a Greek NAFLD Case-Control Study. Nutrients 2024; 16:1235. [PMID: 38674925 PMCID: PMC11055137 DOI: 10.3390/nu16081235] [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: 02/19/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
An ensemble of confounding factors, such as an unhealthy diet, obesity, physical inactivity, and smoking, have been linked to a lifestyle that increases one's susceptibility to chronic diseases and early mortality. The circulatory metabolome may provide a rational means of pinpointing the advent of metabolite variations that reflect an adherence to a lifestyle and are associated with the occurrence of chronic diseases. Data related to four major modifiable lifestyle factors, including adherence to the Mediterranean diet (estimated on MedDietScore), body mass index (BMI), smoking, and physical activity level (PAL), were used to create the lifestyle risk score (LS). The LS was further categorized into four groups, where a higher score group indicates a less healthy lifestyle. Drawing on this, we analyzed 223 NMR serum spectra, 89 MASLD patients and 134 controls; these were coupled to chemometrics to identify "key" features and understand the biological processes involved in specific lifestyles. The unsupervised analysis verified that lifestyle was the factor influencing the samples' differentiation, while the supervised analysis highlighted metabolic signatures. Τhe metabolic ratios of alanine/formic acid and leucine/formic acid, with AUROC > 0.8, may constitute discriminant indexes of lifestyle. On these grounds, this research contributed to understanding the impact of lifestyle on the circulatory metabolome and highlighted "prudent lifestyle" biomarkers.
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Affiliation(s)
- Charalambos Fotakis
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece; (C.F.); (V.A.)
| | - Athina I. Amanatidou
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17671 Athens, Greece; (A.I.A.); (M.K.); (I.P.K.)
| | - Maria Kafyra
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17671 Athens, Greece; (A.I.A.); (M.K.); (I.P.K.)
| | - Vasiliki Andreou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece; (C.F.); (V.A.)
| | - Ioanna Panagiota Kalafati
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17671 Athens, Greece; (A.I.A.); (M.K.); (I.P.K.)
| | - Maria Zervou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece; (C.F.); (V.A.)
| | - George V. Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17671 Athens, Greece; (A.I.A.); (M.K.); (I.P.K.)
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10
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Crossley SWM, Tenney L, Pham VN, Xie X, Zhao MW, Chang CJ. A Transfer Hydrogenation Approach to Activity-Based Sensing of Formate in Living Cells. J Am Chem Soc 2024; 146:8865-8876. [PMID: 38470125 DOI: 10.1021/jacs.3c09735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Formate is a major reactive carbon species in one-carbon metabolism, where it serves as an endogenous precursor for amino acid and nucleic acid biosynthesis and a cellular source of NAD(P)H. On the other hand, aberrant elevations in cellular formate are connected to progression of serious diseases, including cancer and Alzheimer's disease. Traditional methods for formate detection in biological environments often rely on sample destruction or extensive processing, resulting in a loss of spatiotemporal information. To help address these limitations, here we present the design, synthesis, and biological evaluation of a first-generation activity-based sensing system for live-cell formate imaging that relies on iridium-mediated transfer hydrogenation chemistry. Formate facilitates an aldehyde-to-alcohol conversion on various fluorophore scaffolds to enable fluorescence detection of this one-carbon unit, including through a two-color ratiometric response with internal calibration. The resulting two-component probe system can detect changes in formate levels in living cells with a high selectivity over potentially competing biological analytes. Moreover, this activity-based sensing system can visualize changes in endogenous formate fluxes through alterations of one-carbon pathways in cell-based models of human colon cancer, presaging the potential utility of this chemical approach to probe the continuum between one-carbon metabolism and signaling in cancer and other diseases.
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11
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Zwolschen JW, Vos AP, Ariëns RMC, Schols HA. In vitro batch fermentation of (un)saturated homogalacturonan oligosaccharides. Carbohydr Polym 2024; 329:121789. [PMID: 38286556 DOI: 10.1016/j.carbpol.2024.121789] [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: 10/23/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
Pectin, predominantly present within plant cell walls, is a dietary fiber that potentially induces distinct health effects depending on its molecular structure. Such structure-dependent health effects of pectin-derived galacturonic acid oligosaccharides (GalA-OS) are yet largely unknown. This study describes the influence of methyl-esterification and ∆4,5-unsaturation of GalA-OS through defined sets of GalA-OS made from pectin using defined pectinases, on the fermentability by individual fecal inocula. The metabolite production, OS utilization, quantity and size, methyl-esterification and saturation of remaining GalA-OS were monitored during the fermentation of GalA-OS. Fermentation of all GalA-OS predominantly induced the production of acetate, butyrate and propionate. Metabolization of unsaturated GalA-OS (uGalA-OS) significantly increased butyrate formation compared to saturated GalA-OS (satGalA-OS), while satGalA-OS significantly increased propionate formation. Absence of methyl-esters within GalA-OS improved substrate metabolization during the first 18 h of fermentation (99 %) compared to their esterified analogues (51 %). Furthermore, HPAEC and HILIC-LC-MS revealed accumulation of specific methyl-esterified GalA-OS, confirming that methyl-esterification delays fermentation. Fermentation of structurally distinct GalA-OS results in donor specific microbiota composition with uGalA-OS specifically stimulating the butyrate-producer Clostridium Butyricum. This study concludes that GalA-OS fermentation induces highly structure-dependent changes in the gut microbiota, further expanding their potential use as prebiotics.
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Affiliation(s)
- J W Zwolschen
- Wageningen University & Research, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - A P Vos
- Wageningen Food & Biobased Research, Wageningen, the Netherlands
| | - R M C Ariëns
- Wageningen Food & Biobased Research, Wageningen, the Netherlands
| | - H A Schols
- Wageningen University & Research, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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12
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Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey FE, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk RF, Bendlin BB, Hertel J, Thiele I. Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Sci Rep 2024; 14:6095. [PMID: 38480804 PMCID: PMC10937638 DOI: 10.1038/s41598-024-55960-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
In this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimer's disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilised whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalised whole-body metabolic models. Notably, AD individuals displayed diminished formate microbial secretion in these models. Additionally, we identified specific reactions responsible for the production of formate in the host, and interestingly, these reactions were linked to genes that have correlations with AD. This study suggests formate as a possible early AD marker and highlights genetic and microbiome contributions to its production. The reduced formate secretion and its genetic associations point to a complex connection between gut microbiota and AD. This holistic understanding might pave the way for novel diagnostic and therapeutic avenues in AD management.
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Affiliation(s)
- Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
- Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Ann-Kristin Henning
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Maria A Ulmer
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tim Hensen
- School of Medicine, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioural Sciences, Duke University, Durham, NC, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Kathrin Budde
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Corinne D Engelman
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Hans-Jörgen Grabe
- German Center of Neurodegenerative Diseases (DZNE), Rostock/Greifswald, Germany
| | - Margo B Heston
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Sterling Johnson
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ingo Kilimann
- German Center of Neurodegenerative Diseases (DZNE), Rostock, Germany
- Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
| | - Olive Peters
- German Center of Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xiao Wang
- Department of Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Eike Jakob Spruth
- German Center of Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry and Psychotherapy, Charité, Berlin, Germany
| | - Anja Schneider
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Klaus Fliessbach
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Jens Wiltfang
- German Center of Neurodegenerative Diseases (DZNE), Goettingen, Germany
- Department of Psychiatry and Psychotherapy, University of Goettingen, Goettingen, Germany
- Neurosciences and Signaling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Niels Hansen
- Department of Psychiatry and Psychotherapy, University of Goettingen, Goettingen, Germany
| | - Wenzel Glanz
- German Center of Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Katharina Buerger
- German Center of Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Daniel Janowitz
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Christoph Laske
- German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Section for Dementia Research, Hertie Institute for Clinical Brain Research, Tübingen, Germany
- Section for Dementia Research, Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Matthias H Munk
- German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Section for Dementia Research, Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Annika Spottke
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Nina Roy
- German Center of Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Stefan Teipel
- German Center of Neurodegenerative Diseases (DZNE), Rostock, Germany
- Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Engineering, University of California San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | | | - Barbara B Bendlin
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Johannes Hertel
- School of Medicine, University of Galway, Galway, Ireland.
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany.
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland.
- The Ryan Institute, University of Galway, Galway, Ireland.
- School of Microbiology, University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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13
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Lackner S, Mahnert A, Moissl-Eichinger C, Madl T, Habisch H, Meier-Allard N, Kumpitsch C, Lahousen T, Kohlhammer-Dohr A, Mörkl S, Strobl H, Holasek S. Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes-secondary analysis of a randomized placebo-controlled parallel intervention trial. MICROBIOME 2024; 12:49. [PMID: 38461313 PMCID: PMC10924357 DOI: 10.1186/s40168-024-01774-4] [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: 07/11/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints. Given the importance of the gut microbiome in food digestion, we investigated in this secondary analysis of the randomized placebo-controlled parallel intervention study (ClinicalTrials.gov registration: NCT05432362) if aronia juice tolerability was associated with changes in intestinal microbiota and bacterial metabolites, seeking for potential mechanistic insights into the impact on aronia polyphenol tolerance and metabolic outcomes. RESULTS Forty females were enrolled for this 6-week trial, receiving either 100 ml natural aronia juice (verum, V) twice daily or a polyphenol-free placebo (P) with a similar nutritional profile, followed by a 6-week washout. Within V, individuals were categorized into those who tolerated the juice well (Vt) or reported complaints (Vc). The gut microbiome diversity, as analyzed by 16S rRNA gene-based next-generation sequencing, remained unaltered in Vc but changed significantly in Vt. A MICOM-based flux balance analysis revealed pronounced differences in the 40 most predictive metabolites post-intervention. In Vc carbon-dioxide, ammonium and nine O-glycans were predicted due to a shift in microbial composition, while in Vt six bile acids were the most likely microbiota-derived metabolites. NMR metabolomics of plasma confirmed increased lipoprotein subclasses (LDL, VLDL) post-intervention, reverting after wash out. Stool samples maintained a stable metabolic profile. CONCLUSION In linking aronia polyphenol tolerance to gut microbiota-derived metabolites, our study explores adaptive processes affecting lipoprotein profiles during high polyphenol ingestion in Vt and examines effects on mucosal gut health in response to intolerance to high polyphenol intake in Vc. Our results underpin the importance of individualized hormetic dosing for beneficial polyphenol effects, demonstrate dynamic gut microbiome responses to aronia juice, and emphasize personalized responses in polyphenol interventions.
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Affiliation(s)
- Sonja Lackner
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Tobias Madl
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Hansjörg Habisch
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Nathalie Meier-Allard
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Theresa Lahousen
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Alexandra Kohlhammer-Dohr
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Sabrina Mörkl
- Division of Medical Psychology, Psychosomatics and Psychotherapeutic Medicine, Auenbruggerplatz 3, 8036, Graz, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Sandra Holasek
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria.
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14
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Zarou MM, Rattigan KM, Sarnello D, Shokry E, Dawson A, Ianniciello A, Dunn K, Copland M, Sumpton D, Vazquez A, Helgason GV. Inhibition of mitochondrial folate metabolism drives differentiation through mTORC1 mediated purine sensing. Nat Commun 2024; 15:1931. [PMID: 38431691 PMCID: PMC10908830 DOI: 10.1038/s41467-024-46114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Supporting cell proliferation through nucleotide biosynthesis is an essential requirement for cancer cells. Hence, inhibition of folate-mediated one carbon (1C) metabolism, which is required for nucleotide synthesis, has been successfully exploited in anti-cancer therapy. Here, we reveal that mitochondrial folate metabolism is upregulated in patient-derived leukaemic stem cells (LSCs). We demonstrate that inhibition of mitochondrial 1C metabolism through impairment of de novo purine synthesis has a cytostatic effect on chronic myeloid leukaemia (CML) cells. Consequently, changes in purine nucleotide levels lead to activation of AMPK signalling and suppression of mTORC1 activity. Notably, suppression of mitochondrial 1C metabolism increases expression of erythroid differentiation markers. Moreover, we find that increased differentiation occurs independently of AMPK signalling and can be reversed through reconstitution of purine levels and reactivation of mTORC1. Of clinical relevance, we identify that combination of 1C metabolism inhibition with imatinib, a frontline treatment for CML patients, decreases the number of therapy-resistant CML LSCs in a patient-derived xenograft model. Our results highlight a role for folate metabolism and purine sensing in stem cell fate decisions and leukaemogenesis.
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Affiliation(s)
- Martha M Zarou
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Kevin M Rattigan
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Daniele Sarnello
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Engy Shokry
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
| | - Amy Dawson
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Angela Ianniciello
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Karen Dunn
- Paul O'Gorman Leukaemia Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G12 0ZD, UK
| | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G12 0ZD, UK
| | - David Sumpton
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
| | - Alexei Vazquez
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
| | - G Vignir Helgason
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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15
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Barman M, Gio-Batta M, Andrieux L, Stråvik M, Saalman R, Fristedt R, Rabe H, Sandin A, Wold AE, Sandberg AS. Short-chain fatty acids (SCFA) in infants' plasma and corresponding mother's milk and plasma in relation to subsequent sensitisation and atopic disease. EBioMedicine 2024; 101:104999. [PMID: 38340558 PMCID: PMC10869761 DOI: 10.1016/j.ebiom.2024.104999] [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: 07/02/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Short-chain fatty acids (SCFAs) in intestinal contents may influence immune function, while less is known about SCFAs in blood plasma. The aims were to investigate the relation between infants' and maternal plasma SCFAs, as well as SCFAs in mother's milk, and relate SCFA concentrations in infant plasma to subsequent sensitisation and atopic disease. METHODS Infant plasma (N = 148) and corresponding mother's milk and plasma were collected four months postpartum. Nine SCFA (formic, acetic, propionic, isobutyric, butyric, succinic, valeric, isovaleric, and caproic acid) were analysed by UPLC-MS. At 12 months of age, atopic disease was diagnosed by a pediatric allergologist, and sensitisation was measured by skin prick test. All families participated in the Swedish birth cohort NICE (Nutritional impact on Immunological maturation during Childhood in relation to the Environment). FINDINGS Infants with sensitisation, atopic eczema, or food allergy had significantly lower concentrations of five, three, and two SCFAs, respectively, in plasma at four months. Logistic regressions models showed significant negative associations between formic, succinic, and caproic acid and sensitisation [ORadj (95% CI) per SD: 0.41 (0.19-0.91); 0.19 (0.05-0.75); 0.25 (0.09-0.66)], and between acetic acid and atopic eczema [0.42 (0.18-0.95)], after adjusting for maternal allergy. Infants' and maternal plasma SCFA concentrations correlated strongly, while milk SCFA concentrations were unrelated to both. Butyric and caproic acid concentrations were enriched around 100-fold, and iso-butyric and valeric acid around 3-5-fold in mother's milk, while other SCFAs were less prevalent in milk than in plasma. INTERPRETATION Butyric and caproic acid might be actively transported into breast milk to meet the needs of the infant, although mechanistic studies are needed to confirm this. The negative associations between certain SCFAs on sensitisation and atopic disease adds to prior evidence regarding their immunoregulatory potential. FUNDING Swedish Research Council (Nr. 2013-3145, 2019-0137 and 2023-02217 to A-S.S.), Swedish Research Council for Health, Working Life and Welfare FORTE, Nr 2018-00485 to A.W.), The Swedish Asthma and Allergy Association's Research Fund (2020-0020 to A.S.).
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Affiliation(s)
- Malin Barman
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, Gothenburg 412 96, Sweden.
| | - Monica Gio-Batta
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Léna Andrieux
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, Gothenburg 412 96, Sweden; Département de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69342 Lyon Cedex 07, France
| | - Mia Stråvik
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Robert Saalman
- Institute of Clinical Sciences, Department of Pediatrics, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Rikard Fristedt
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Hardis Rabe
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Anna Sandin
- Department of Clinical Science, Pediatrics, Sunderby Research Unit, Umeå University, Umeå 901 87, Sweden
| | - Agnes E Wold
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Ann-Sofie Sandberg
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, Gothenburg 412 96, Sweden
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16
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Shurubor YI, Krasnikov AB, Isakova EP, Deryabina YI, Yudin VS, Keskinov AA, Krasnikov BF. Energy Metabolites and Indicative Significance of α-Ketoglutarate and α-Ketoglutaramate in Assessing the Progression of Chronic Hepatoencephalopathy. Biomolecules 2024; 14:217. [PMID: 38397454 PMCID: PMC10887089 DOI: 10.3390/biom14020217] [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: 12/20/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In the example of a rat model with chronic hepatoencephalopathy (HE), changes in the organ morphology of rats affect the balance of metabolites of the tricarboxylic acid (TCA) cycle and metabolites of the glutamine-glutamate (Gln-Glu) cycle, namely α-ketoglutarate (αKG) and α-ketoglutaramate (αKGM), as well as the enzymes associated with them, ω-amidase (ωA) and glutamine transaminase (GTK). This model of rats was obtained as a result of 2-22 weeks of consumption by animals of hepatotoxin thioacetamide (TAA) added to drinking water at a concentration of 0.4 g/L. The control (n = 26) and TAA-induced (n = 55) groups of rats consisted of 11 cohorts each. The control cohorts consisted of 2-4 rats, and the TAA-induced cohorts consisted of 4-7 individuals. Every two weeks, samples of blood plasma, liver, kidney, and brain tissues were taken from the next cohort of rats (a total of 320 samples). By the end of the experiment, irreversible morphological changes were observed in the organs of rats: the weight of the animals was reduced up to ~45%, the weight of the kidneys up to 5%, the brain up to ~20%, and the weight of the liver increased up to ~20%. The analysis revealed: (i) a decrease in the activity of ωA and GTK in the tissues of the brain, kidneys, and liver of rats with chronic HE (by ~3, 40, and 65% and ~10, 60, and 70%, respectively); and (ii) the appearance of a significant imbalance in the content of metabolites of the Gln-Glu cycle, αKG, and αKGM. It is indicative that a ~1.5-12-fold increase in the level of αKG in the blood plasma and tissues of the organs of rats with chronic HE was accompanied by a synchronous, ~1.2-2.5-fold decrease in the level of αKGM. The data obtained indicate an essential involvement of the Gln-Glu cycle in the regulation of energy metabolism in rats under conditions of chronic HE. Attention is focused on the significance of the αKG/αKGM ratio, which can act as a potential marker for diagnosing the degree of HE development.
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Affiliation(s)
- Yevgeniya I. Shurubor
- Centre for Strategic Planning of FMBA of Russia, Pogodinskaya St., Bld. 10, 119121 Moscow, Russia; (Y.I.S.); (V.S.Y.); (A.A.K.)
| | | | - Elena P. Isakova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (E.P.I.); (Y.I.D.)
| | - Yulia I. Deryabina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (E.P.I.); (Y.I.D.)
| | - Vladimir S. Yudin
- Centre for Strategic Planning of FMBA of Russia, Pogodinskaya St., Bld. 10, 119121 Moscow, Russia; (Y.I.S.); (V.S.Y.); (A.A.K.)
| | - Anton A. Keskinov
- Centre for Strategic Planning of FMBA of Russia, Pogodinskaya St., Bld. 10, 119121 Moscow, Russia; (Y.I.S.); (V.S.Y.); (A.A.K.)
| | - Boris F. Krasnikov
- Centre for Strategic Planning of FMBA of Russia, Pogodinskaya St., Bld. 10, 119121 Moscow, Russia; (Y.I.S.); (V.S.Y.); (A.A.K.)
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, N.I. Pirogov Russian National Research Medical University, 1 Ostrovitianova Str., 117997 Moscow, Russia
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Thing M, Werge MP, Kimer N, Hetland LE, Rashu EB, Nabilou P, Junker AE, Galsgaard ED, Bendtsen F, Laupsa-Borge J, McCann A, Gluud LL. Targeted metabolomics reveals plasma short-chain fatty acids are associated with metabolic dysfunction-associated steatotic liver disease. BMC Gastroenterol 2024; 24:43. [PMID: 38262952 PMCID: PMC10804800 DOI: 10.1186/s12876-024-03129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Alterations in the production of short-chain fatty acids (SCFAs) may reflect disturbances in the gut microbiota and have been linked to metabolic dysfunction-associated steatotic liver disease (MASLD). We assessed plasma SCFAs in patients with MASLD and healthy controls. METHODS Fasting venous blood samples were collected and eight SCFAs were measured using gas chromatography-tandem mass spectrometry (GC-MS/MS). Relative between-group differences in circulating SCFA concentrations were estimated by linear regression, and the relation between SCFA concentrations, MASLD, and fibrosis severity was investigated using logistic regression. RESULTS The study includes 100 patients with MASLD (51% with mild/no fibrosis and 49% with significant fibrosis) and 50 healthy controls. Compared with healthy controls, MASLD patients had higher plasma concentrations of propionate (21.8%, 95% CI 3.33 to 43.6, p = 0.02), formate (21.9%, 95% CI 6.99 to 38.9, p = 0.003), valerate (35.7%, 95% CI 4.53 to 76.2, p = 0.02), and α-methylbutyrate (16.2%, 95% CI 3.66 to 30.3, p = 0.01) but lower plasma acetate concentrations (- 30.0%, 95% CI - 40.4 to - 17.9, p < 0.001). Among patients with MASLD, significant fibrosis was positively associated with propionate (p = 0.02), butyrate (p = 0.03), valerate (p = 0.03), and α-methylbutyrate (p = 0.02). Six of eight SCFAs were significantly increased in F4 fibrosis. CONCLUSIONS In the present study, SCFAs were associated with MASLD and fibrosis severity, but further research is needed to elucidate the potential mechanisms underlying our observations and to assess the possible benefit of therapies modulating gut microbiota.
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Affiliation(s)
- Mira Thing
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | - Mikkel Parsberg Werge
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | - Nina Kimer
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | - Liv Eline Hetland
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | - Elias Badal Rashu
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | - Puria Nabilou
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | - Anders Ellekaer Junker
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | | | - Flemming Bendtsen
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark
| | | | | | - Lise Lotte Gluud
- Gastro Unit, Copenhagen University Hospital Hvidovre, Kettegard Alle 30, Hvidovre, 2650, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark.
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18
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Cifuentes MP, Chapman JA, Stewart CJ. Gut microbiome derived short chain fatty acids: Promising strategies in necrotising enterocolitis. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100219. [PMID: 38303965 PMCID: PMC10831176 DOI: 10.1016/j.crmicr.2024.100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
Necrotising enterocolitis (NEC) is a devastating condition that poses a significant risk of morbidity and mortality, particularly among preterm babies. Extensive research efforts have been directed at identifying optimal treatment and diagnostic strategies but results from such studies remain unclear and controversial. Among the most promising candidates are prebiotics, probiotics and their metabolites, including short chain fatty acids (SCFAs). Such metabolites have been widely explored as possible biomarkers of gut health for different clinical conditions, with overall positive effects on the host observed. This review aims to describe the role of gut microbiome derived SCFAs in necrotising enterocolitis. Until now, information has been conflicting, with the primary focus on the main three SCFAs (acetic acid, propionic acid, and butyric acid). While numerous studies have indicated the relationship between SCFAs and NEC, the current evidence is insufficient to draw definitive conclusions about the use of these metabolites as NEC biomarkers or their potential in treatment strategies. Ongoing research in this area will help enhance both our understanding of SCFAs as valuable indicators of NEC and their practical application in clinical settings.
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Affiliation(s)
- María P Cifuentes
- Translational and Clinical Research Institute, Newcastle University, Newcastle. UK
| | - Jonathan A Chapman
- Translational and Clinical Research Institute, Newcastle University, Newcastle. UK
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19
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Ramirez-Hernandez G, Kory N. Exquisite exposure: Formaldehyde as a metabolic regulator. Mol Cell 2024; 84:20-22. [PMID: 38181762 DOI: 10.1016/j.molcel.2023.12.006] [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: 12/08/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Throughout life, whether through external consumption or internal production, we are exposed to different reactive metabolites considered toxic to the body. Pham et al.1 uncover metabolic regulation by one such harmful metabolite: formaldehyde.
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Affiliation(s)
| | - Nora Kory
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cancer Cell Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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20
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Zheng BS, Wang SD, Zhang JY, Ge CG. Expression, Prognostic Value, and Immune Infiltration of MTHFD Family in Bladder Cancer. Curr Cancer Drug Targets 2024; 24:178-191. [PMID: 37539926 DOI: 10.2174/1568009623666230804152603] [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: 04/18/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND The Methylenetetrahydrofolate Dehydrogenase (MTHFD) family plays an important role in the development and prognosis of a variety of tumors; however, the role of the MTHFD family in bladder cancer is unclear. METHODS R software, cBioPortal, GeneMANIA, and online sites such as String-LinkedOmics were used for bioinformatics analysis. RESULTS MTHFD1/1L/2 was significantly upregulated in bladder cancer tissues compared with normal tissues, high expression of the MTHFD family was strongly associated with poorer clinical grading and staging, and bladder cancer patients with upregulated expression of MTHFD1L/2 had a significantly worse prognosis. Gene function and PPI network analysis revealed that the MTHFD family and related genes play synergistic roles in the development of bladder cancer. 800 co-expressed genes related to the MTHFD family were used for functional enrichment analysis, and the results showed that many genes were associated with various oncogenic pathways such as cell cycle and DNA replication. More importantly, the MTHFD family was closely associated with multiple infiltrating immune lymphocytes, including Treg cells, and immune molecules such as TNFSF9, CD274, and PDCD1. CONCLUSION Our study shows that MTHFD family genes may be potential prognostic markers and therapeutic targets for patients with bladder cancer.
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Affiliation(s)
- Bai Shu Zheng
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Shun De Wang
- Department of Urology, The ChenJiaqiao Hospital of ShaPingba District of Chongqing City, Chongqing, 401331, China
| | - Jun Yong Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Cheng Guo Ge
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
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21
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Ren X, Wang X, Zheng G, Wang S, Wang Q, Yuan M, Xu T, Xu J, Huang P, Ge M. Targeting one-carbon metabolism for cancer immunotherapy. Clin Transl Med 2024; 14:e1521. [PMID: 38279895 PMCID: PMC10819114 DOI: 10.1002/ctm2.1521] [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: 08/01/2023] [Revised: 11/15/2023] [Accepted: 12/10/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND One-carbon (1C) metabolism is a metabolic network that plays essential roles in biological reactions. In 1C metabolism, a series of nutrients are used to fuel metabolic pathways, including nucleotide metabolism, amino acid metabolism, cellular redox defence and epigenetic maintenance. At present, 1C metabolism is considered the hallmark of cancer. The 1C units obtained from the metabolic pathways increase the proliferation rate of cancer cells. In addition, anticancer drugs, such as methotrexate, which target 1C metabolism, have long been used in the clinic. In terms of immunotherapy, 1C metabolism has been used to explore biomarkers connected with immunotherapy response and immune-related adverse events in patients. METHODS We collected numerous literatures to explain the roles of one-carbon metabolism in cancer immunotherapy. RESULTS In this review, we focus on the important pathways in 1C metabolism and the function of 1C metabolism enzymes in cancer immunotherapy. Then, we summarise the inhibitors acting on 1C metabolism and their potential application on cancer immunotherapy. Finally, we provide a viewpoint and conclusion regarding the opportunities and challenges of targeting 1C metabolism for cancer immunotherapy in clinical practicability in the future. CONCLUSION Targeting one-carbon metabolism is useful for cancer immunotherapy.
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Affiliation(s)
- Xinxin Ren
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
- Department of PathologyCancer CenterZhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiang Wang
- Department of PharmacyAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiangChina
| | - Guowan Zheng
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Shanshan Wang
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Qiyue Wang
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Mengnan Yuan
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Tong Xu
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Jiajie Xu
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Ping Huang
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Minghua Ge
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
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22
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Pinto S, Guerra-Carvalho B, Crisóstomo L, Rocha A, Barros A, Alves MG, Oliveira PF. Metabolomics Integration in Assisted Reproductive Technologies for Enhanced Embryo Selection beyond Morphokinetic Analysis. Int J Mol Sci 2023; 25:491. [PMID: 38203668 PMCID: PMC10778973 DOI: 10.3390/ijms25010491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/12/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Embryo quality evaluation during in vitro development is a crucial factor for the success of assisted reproductive technologies (ARTs). However, the subjectivity inherent in the morphological evaluation by embryologists can introduce inconsistencies that impact the optimal embryo choice for transfer. To provide a more comprehensive evaluation of embryo quality, we undertook the integration of embryo metabolomics alongside standardized morphokinetic classification. The culture medium of 55 embryos (derived from 21 couples undergoing ICSI) was collected at two timepoints (days 3 and 5). Samples were split into Good (n = 29), Lagging (n = 19), and Bad (n = 10) according to embryo morphokinetic evaluation. Embryo metabolic performance was assessed by monitoring the variation in specific metabolites (pyruvate, lactate, alanine, glutamine, acetate, formate) using 1H-NMR. Adjusted metabolite differentials were observed during the first 3 days of culture and found to be discriminative of embryo quality at the end of day 5. Pyruvate, alanine, glutamine, and acetate were major contributors to this discrimination. Good and Lagging embryos were found to export and accumulate pyruvate and glutamine in the first 3 days of culture, while Bad embryos consumed them. This suggests that Bad embryos have less active metabolic activity than Good and Lagging embryos, and these two metabolites are putative biomarkers for embryo quality. This study provides a more comprehensive evaluation of embryo quality and can lead to improvements in ARTs by enabling the selection of the best embryos. By combining morphological assessment and metabolomics, the selection of high-quality embryos with the potential to result in successful pregnancies may become more accurate and consistent.
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Affiliation(s)
- Soraia Pinto
- Centre for Reproductive Genetics Alberto Barros, 4100-012 Porto, Portugal; (S.P.); (A.B.)
| | | | - Luís Crisóstomo
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland;
| | - António Rocha
- CECA/ICETA–Centro de Estudos de Ciência Animal, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4200-135 Porto, Portugal;
| | - Alberto Barros
- Centre for Reproductive Genetics Alberto Barros, 4100-012 Porto, Portugal; (S.P.); (A.B.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Marco G. Alves
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Pedro F. Oliveira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
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23
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Lin MC, Moller SH, Ho PC. Re-"Formate" T-cell Antitumor Responses. Cancer Discov 2023; 13:2507-2509. [PMID: 38084093 DOI: 10.1158/2159-8290.cd-23-1059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
SUMMARY Rowe and colleagues discover that one-carbon (1C) metabolism rewiring occurs upon T-cell activation to support proliferation and cytolytic activity in CD8+ T cells and that supplementation of 1C donor formate rescues the dysfunctional T cells and their responsiveness to anti-PD-1 in selective tumor-infiltrated T-cell subsets. This finding represents an attractive strategy to overcome a metabolic vulnerability in the tumor microenvironment and improve the efficacy of immune checkpoint blockade. See related article by Rowe et al., p. 2566 (8).
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Affiliation(s)
- Mei-Chun Lin
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sofie Hedlund Moller
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
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24
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Oliveira N, Sousa A, Amaral AP, Graça G, Verde I. Searching for Metabolic Markers of Stroke in Human Plasma via NMR Analysis. Int J Mol Sci 2023; 24:16173. [PMID: 38003362 PMCID: PMC10671802 DOI: 10.3390/ijms242216173] [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: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
More than 12 million people around the world suffer a stroke every year, one every 3 s. Stroke has a variety of causes and is often the result of a complex interaction of risk factors related to age, genetics, gender, lifestyle, and some cardiovascular and metabolic diseases. Despite this evidence, it is not possible to prevent the onset of stroke. The use of innovative methods for metabolite analysis has been explored in the last years to detect new stroke biomarkers. We use NMR spectroscopy to identify small molecule variations between different stages of stroke risk. The Framingham Stroke Risk Score was used in people over 63 years of age living in long-term care facilities (LTCF) to calculate the probability of suffering a stroke. Using this parameter, three study groups were formed: low stroke risk (LSR, control), moderate stroke risk (MSR) and high stroke risk (HSR). Univariate statistical analysis showed seven metabolites with increasing plasma levels across different stroke risk groups, from LSR to HSR: isoleucine, asparagine, formate, creatinine, dimethylsulfone and two unidentified molecules, which we termed "unknown-1" and "unknown-3". These metabolic markers can be used for early detection and to detect increasing stages of stroke risk more efficiently.
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Affiliation(s)
- Nádia Oliveira
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior (UBI), Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (N.O.); (A.S.); (A.P.A.)
| | - Adriana Sousa
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior (UBI), Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (N.O.); (A.S.); (A.P.A.)
| | - Ana Paula Amaral
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior (UBI), Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (N.O.); (A.S.); (A.P.A.)
| | - Gonçalo Graça
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ignacio Verde
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior (UBI), Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (N.O.); (A.S.); (A.P.A.)
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25
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Kutschka I, Bertero E, Wasmus C, Xiao K, Yang L, Chen X, Oshima Y, Fischer M, Erk M, Arslan B, Alhasan L, Grosser D, Ermer KJ, Nickel A, Kohlhaas M, Eberl H, Rebs S, Streckfuss-Bömeke K, Schmitz W, Rehling P, Thum T, Higuchi T, Rabinowitz J, Maack C, Dudek J. Activation of the integrated stress response rewires cardiac metabolism in Barth syndrome. Basic Res Cardiol 2023; 118:47. [PMID: 37930434 PMCID: PMC10628049 DOI: 10.1007/s00395-023-01017-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/29/2023] [Accepted: 10/14/2023] [Indexed: 11/07/2023]
Abstract
Barth Syndrome (BTHS) is an inherited cardiomyopathy caused by defects in the mitochondrial transacylase TAFAZZIN (Taz), required for the synthesis of the phospholipid cardiolipin. BTHS is characterized by heart failure, increased propensity for arrhythmias and a blunted inotropic reserve. Defects in Ca2+-induced Krebs cycle activation contribute to these functional defects, but despite oxidation of pyridine nucleotides, no oxidative stress developed in the heart. Here, we investigated how retrograde signaling pathways orchestrate metabolic rewiring to compensate for mitochondrial defects. In mice with an inducible knockdown (KD) of TAFAZZIN, and in induced pluripotent stem cell-derived cardiac myocytes, mitochondrial uptake and oxidation of fatty acids was strongly decreased, while glucose uptake was increased. Unbiased transcriptomic analyses revealed that the activation of the eIF2α/ATF4 axis of the integrated stress response upregulates one-carbon metabolism, which diverts glycolytic intermediates towards the biosynthesis of serine and fuels the biosynthesis of glutathione. In addition, strong upregulation of the glutamate/cystine antiporter xCT increases cardiac cystine import required for glutathione synthesis. Increased glutamate uptake facilitates anaplerotic replenishment of the Krebs cycle, sustaining energy production and antioxidative pathways. These data indicate that ATF4-driven rewiring of metabolism compensates for defects in mitochondrial uptake of fatty acids to sustain energy production and antioxidation.
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Affiliation(s)
- Ilona Kutschka
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Edoardo Bertero
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
- Department of Internal Medicine, University of Genova, Genoa, Italy
- Cardiovascular Disease Unit, IRCCS Ospedale Policlinico San Martino - Italian IRCCS Cardiology Network, Genoa, Italy
| | - Christina Wasmus
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Lifeng Yang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Rd, Shanghai, 200031, China
| | - Xinyu Chen
- Department of Nuclear Medicine, University Clinic Würzburg, Oberdürrbacher Strasse 6, 97080, Würzburg, Germany
| | - Yasuhiro Oshima
- Department of Nuclear Medicine, University Clinic Würzburg, Oberdürrbacher Strasse 6, 97080, Würzburg, Germany
| | - Marcus Fischer
- Division of Pediatric Cardiology and Intensive Care, University Hospital LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Manuela Erk
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Berkan Arslan
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Lin Alhasan
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Daria Grosser
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Katharina J Ermer
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Alexander Nickel
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Michael Kohlhaas
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
| | - Hanna Eberl
- Department for Pharmacology and Toxicology, University of Würzburg, Versbacher Strasse 9, 97078, Würzburg, Germany
| | - Sabine Rebs
- Department for Pharmacology and Toxicology, University of Würzburg, Versbacher Strasse 9, 97078, Würzburg, Germany
| | - Katrin Streckfuss-Bömeke
- Department for Pharmacology and Toxicology, University of Würzburg, Versbacher Strasse 9, 97078, Würzburg, Germany
- Clinic for Cardiology and Pneumology, Georg-August University Göttingen and DZHK (German Center for Cardiovascular Research), Partner Site, Göttingen, Germany
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Peter Rehling
- University Göttingen, Institute of Biochemistry and Molecular Cell Biology, Humboldtallee 23, 37072, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
- Rebirth Center for Translational Regenerative Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Takahiro Higuchi
- Department of Nuclear Medicine, University Clinic Würzburg, Oberdürrbacher Strasse 6, 97080, Würzburg, Germany
| | - Joshua Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Christoph Maack
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany
- Medical Clinic I, University Clinic Würzburg, Würzburg, Germany
| | - Jan Dudek
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Am Schwarzenberg 15, Haus A15, 97078, Würzburg, Germany.
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Ghini V, Vieri W, Celli T, Pecchioli V, Boccia N, Alonso-Vásquez T, Pelagatti L, Fondi M, Luchinat C, Bertini L, Vannucchi V, Landini G, Turano P. COVID-19: A complex disease with a unique metabolic signature. PLoS Pathog 2023; 19:e1011787. [PMID: 37943960 PMCID: PMC10662774 DOI: 10.1371/journal.ppat.1011787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/21/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Plasma of COVID-19 patients contains a strong metabolomic/lipoproteomic signature, revealed by the NMR analysis of a cohort of >500 patients sampled during various waves of COVID-19 infection, corresponding to the spread of different variants, and having different vaccination status. This composite signature highlights common traits of the SARS-CoV-2 infection. The most dysregulated molecules display concentration trends that scale with disease severity and might serve as prognostic markers for fatal events. Metabolomics evidence is then used as input data for a sex-specific multi-organ metabolic model. This reconstruction provides a comprehensive view of the impact of COVID-19 on the entire human metabolism. The human (male and female) metabolic network is strongly impacted by the disease to an extent dictated by its severity. A marked metabolic reprogramming at the level of many organs indicates an increase in the generic energetic demand of the organism following infection. Sex-specific modulation of immune response is also suggested.
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Affiliation(s)
- Veronica Ghini
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Walter Vieri
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tommaso Celli
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Valentina Pecchioli
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Nunzia Boccia
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Tania Alonso-Vásquez
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Lorenzo Pelagatti
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino Florence, Italy
| | - Laura Bertini
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Vieri Vannucchi
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Giancarlo Landini
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Paola Turano
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino Florence, Italy
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Guzzardi MA, La Rosa F, Granziera F, Panetta D, Pardo-Tendero M, Barone M, Turroni S, Faita F, Kusmic C, Brigidi P, Monleon D, Iozzo P. Gut-derived metabolites mediating cognitive development in 5-year-old children: Early-life transplant in mice has lasting effects throughout adulthood. Brain Behav Immun 2023; 114:94-110. [PMID: 37557963 DOI: 10.1016/j.bbi.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023] Open
Abstract
The gut microbiota has been causally linked to cognitive development. We aimed to identify metabolites mediating its effect on cognitive development, and foods or nutrients related to most promising metabolites. Faeces from 5-year-old children (DORIAN-PISAC cohort, including 90 general population families with infants, 42/48 females/males, born in 2011-2014) were transplanted (FMT) into C57BL/6 germ-free mice. Children and recipient mice were stratified by cognitive phenotype, or based on protective metabolites. Food frequency questionnaires were obtained in children. Cognitive measurements in mice included five Y-maze tests until 23 weeks post-FMT, and (at 23 weeks) PET-CT for brain metabolism and radiodensity, and ultrasound-based carotid vascular indices. Children (faeces, urine) and mice (faeces, plasma) metabolome was measured by 1H NMR spectroscopy, and the faecal microbiota was profiled in mice by 16S rRNA amplicon sequencing. Cognitive scores of children and recipient mice were correlated. FMT-dependent modifications of brain metabolism were observed. Mice receiving FMT from high-cognitive or protective metabolite-enriched children developed superior cognitive-behavioural performance. A panel of metabolites, namely xanthine, hypoxanthine, formate, mannose, tyrosine, phenylalanine, glutamine, was found to mediate the gut-cognitive axis in donor children and recipient mice. Vascular indices partially explained the metabolite-to-phenotype relationships. Children's consumption of legumes, whole-milk yogurt and eggs, and intake of iron, zinc and vitamin D appeared to support protective gut metabolites. Overall, metabolites involved in inflammation, purine metabolism and neurotransmitter synthesis mediate the gut-cognitive axis, and holds promise for screening. The related dietary and nutritional findings offer leads to microbiota-targeted interventions for cognitive protection, with long-lasting effects.
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Affiliation(s)
- Maria Angela Guzzardi
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy.
| | - Federica La Rosa
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy.
| | - Federico Granziera
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy; Sant'Anna School of Advanced Studies, 56127 Pisa, Italy.
| | - Daniele Panetta
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy.
| | - Mercedes Pardo-Tendero
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy; Faculty of Medicine, University of Valencia, Health Research Institute INCLIVA/CIBERFES for Frailty and Healthy Aging, 46010 Valencia, Spain.
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy.
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
| | - Francesco Faita
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy.
| | - Claudia Kusmic
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy.
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy.
| | - Daniel Monleon
- Faculty of Medicine, University of Valencia, Health Research Institute INCLIVA/CIBERFES for Frailty and Healthy Aging, 46010 Valencia, Spain.
| | - Patricia Iozzo
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 56124 Pisa, Italy.
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Jeon YH, Lee S, Kim DW, Kim S, Bae SS, Han M, Seong EY, Song SH. Serum and urine metabolomic biomarkers for predicting prognosis in patients with immunoglobulin A nephropathy. Kidney Res Clin Pract 2023; 42:591-605. [PMID: 37448290 PMCID: PMC10565460 DOI: 10.23876/j.krcp.22.146] [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: 07/07/2022] [Revised: 11/09/2022] [Accepted: 11/28/2022] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Immunoglobulin A nephropathy (IgAN) is the most prevalent form of glomerulonephritis worldwide. Prediction of disease progression in IgAN can help to provide individualized treatment based on accurate risk stratification. METHODS We performed proton nuclear magnetic resonance-based metabolomics analyses of serum and urine samples from healthy controls, non-progressor (NP), and progressor (P) groups to identify metabolic profiles of IgAN disease progression. Metabolites that were significantly different between the NP and P groups were selected for pathway analysis. Subsequently, we analyzed multivariate area under the receiver operating characteristic (ROC) curves to evaluate the predictive power of metabolites associated with IgAN progression. RESULTS We observed several distinct metabolic fingerprints of the P group involving the following metabolic pathways: glycolipid metabolism; valine, leucine, and isoleucine biosynthesis; aminoacyl-transfer RNA biosynthesis; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism. In multivariate ROC analyses, the combinations of serum glycerol, threonine, and proteinuria (area under the curve [AUC], 0.923; 95% confidence interval [CI], 0.667-1.000) and of urinary leucine, valine, and proteinuria (AUC, 0.912; 95% CI, 0.667-1.000) showed the highest discriminatory ability to predict IgAN disease progression. CONCLUSION This study identified serum and urine metabolites profiles that can aid in the identification of progressive IgAN and proposed perturbed metabolic pathways associated with the identified metabolites.
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Affiliation(s)
- You Hyun Jeon
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Sujin Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, Republic of Korea
| | - Da Woon Kim
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, Republic of Korea
| | - Sun Sik Bae
- Department of Pharmacology, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Miyeun Han
- Division of Nephrology, Department of Internal Medicine, National Medical Center, Seoul, Republic of Korea
| | - Eun Young Seong
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Sang Heon Song
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
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Hu L, Brito LF, Luo H, Chen S, Johnson JS, Sammad A, Guo G, Xu Q, Wang Y. Differential Responses of Physiological Parameters, Production Traits, and Blood Metabolic Profiling between First- and Second-Parity Holstein Cows in the Comparison of Spring versus Summer Seasons. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11902-11920. [PMID: 37490609 DOI: 10.1021/acs.jafc.3c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Heat stress (HS) negatively influences cows' welfare and productivity. Therefore, a better understanding of the physiological and molecular mechanisms of HS responses from multiple parities is paramount for the development of effective management and breeding strategies. In comparison with first-parity cows in the spring (Spring-1), first-parity cows in the summer (Summer-1) had a significantly higher rectal temperature (RT), respiration rate (RR), drooling score (DS), and daily activity (DA), while lower (P < 0.05) daily rumination (DR), seven-day average milk yield (7AMY), milk yield on sampling day (MY_S), milk yield on test day (MY_T), and lactose percentage (LP) were observed. When comparing the spring (Spring-2) and summer (Summer-2) of the second-parity cows, significant differences were also found in RT, RR, DS, DA, and DR (P < 0.05), corresponding to similar trends with the first parity while having smaller changes. Moreover, significantly negative impacts on performance traits were only observed on fat percentage (FP) and LP. These results showed that there were different biological responses between first- and second-parity Holstein cows. Further, 18 and 17 metabolites were involved in the seasonal response of first- and second-parity cows, respectively. Nine differential metabolites were shared between the two parities, and pathway analyses suggested that cows had an inhibited tricarboxylic acid cycle, increased utilization of lipolysis, and a dysregulated gut microbiome during the summer. The metabolites identified exclusively for each parity highlighted the differences in microbial response and host amino acid metabolism between two parities in response to HS. Moreover, glucose, ethanol, and citrate were identified as potential biomarkers for distinguishing individuals between Spring-1 and Summer-1. Ethanol and acetone were better predictors for distinguishing individuals between Spring-2 and Summer-2. Taken together, the present study demonstrated the impact of naturally induced HS on physiological parameters, production traits, and the blood metabolome of Holstein cows. There are different biological responses and regulation mechanisms between first- and second-parity Holstein cows.
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Affiliation(s)
- Lirong Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hanpeng Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shaokan Chen
- Beijing Sunlon Livestock Development Co. Ltd, Beijing 100176, China
| | - Jay S Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, Indiana 47907, United States
| | - Abdul Sammad
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing 100176, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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30
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Lee J, Jeong HJ, Kim H, Park JS. The Role of the Bile Microbiome in Common Bile Duct Stone Development. Biomedicines 2023; 11:2124. [PMID: 37626621 PMCID: PMC10452286 DOI: 10.3390/biomedicines11082124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
INTRODUCTION Common bile duct (CBD) stones are a health concern for 10-20% of individuals with symptomatic gallstones, leading to health complications and placing a burden on healthcare systems. This study was initiated to investigate the changes in microbiome compositions and the metabolic signature associated with CBD stones. The research approach integrated taxonomic and functional data with metabolomics data, complemented by in vivo experiments. METHODS In a single tertiary healthcare institution, a total of 25 patients were enrolled who had undergone endoscopic retrograde cholangiopancreatography (ERCP) between February 2019 and January 2021. We harvested DNA from bile samples acquired from these individuals. The amplification of the bacterial 16S rRNA gene V3-V4 region was conducted through polymerase chain reaction (PCR), followed by sequencing. We utilized QIIME2 for a comprehensive data analysis. Furthermore, we performed a metabolomic analysis of the bile samples using nuclear magnetic resonance (NMR) spectroscopy. For the assessment of functional gene enrichment, we employed MetaboAnalyst 5.0. Lastly, we executed in vivo experiments on C57BL/6 mice and undertook histological examinations of tissue samples. RESULTS Out of the 25 study subjects, 17 underwent ERCP due to CBD stones (the CBD stone group), while the remaining 8 had the procedure for different reasons (the non-CBD stone group). An alpha diversity analysis showed a significantly greater microbial diversity in the bile samples of the non-CBD stone group (p < 0.01), and a beta diversity analysis confirmed the greater microbial compositional abundance in the gut microbiomes in this group (p = 0.01). A taxonomic analysis revealed that the abundances of Enterococcaceae and Enterococcus were higher in the bile microbiomes of the CBD stone group. A metabolic profile analysis showed that the acetate, formate, and asparagine levels were higher in the CBD stone group. A pathway enrichment analysis showed the metabolic pathways (Arginine and Proline Metabolism, Aspartate Metabolism, Glycine, and Serine Metabolism, and Ammonia Recycling pathways) that were associated with these differences. Preclinical experiments demonstrated systemic inflammation and extracellular trap formation in the CBD stone group. CONCLUSIONS Our study highlights the importance of biliary dysbiosis and bile metabolites, specifically acetate and formate, in CBD stone development and progression. These findings have implications for the development of diagnostic and therapeutic strategies using microbiomes for CBD stones.
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Affiliation(s)
| | | | | | - Jin-Seok Park
- Digestive Disease Center, Department of Internal Medicine, Inha University College of Medicine, Inha University Hospital, Incheon 22332, Republic of Korea; (J.L.); (H.J.J.); (H.K.)
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Packi K, Matysiak J, Plewa S, Klupczyńska-Gabryszak A, Matuszewska E, Rzetecka N, Bręborowicz A, Matysiak J. Amino Acid Profiling Identifies Disease-Specific Signatures in IgE-Mediated and Non-IgE-Mediated Food Allergy in Pediatric Patients with Atopic Dermatitis. Biomedicines 2023; 11:1919. [PMID: 37509558 PMCID: PMC10377369 DOI: 10.3390/biomedicines11071919] [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: 06/02/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
An IgE-mediated food allergy (FA) in atopic dermatitis (AD) children should be easily differentiated from other immune-mediated adverse effects related to food. Specific IgEs for particular protein components has provided additional diagnostic value. However, component-resolved diagnostics (CRD) has not solved all diagnostic problems either. We analysed the serum profile of 42 amino acids (AAs) in 76 AD children aged 2-60 months with an IgE-mediated FA (n = 36), with a non-IgE-mediated FA (n = 15) and without an FA (n = 25) using high-performance liquid chromatography coupled with mass spectrometry (LC-MS/MS) and an aTRAQ kit. We identified homocitrulline (Hcit), sarcosine (Sar) and L-tyrosine (Tyr) as features that differentiated the studied groups (one-way ANOVA with least significant difference post hoc test). The Hcit concentrations in the non-IgE-mediated FA group were significantly decreased compared with the IgE-mediated FA group (p = 0.018) and the control group (p = 0.008). In AD children with a non-IgE-mediated FA, the Tyr levels were also significantly reduced compared with the controls (p = 0.009). The mean concentration of Sar was the highest in the non-IgE-mediated FA group and the lowest in the IgE-mediated FA group (p = 0.047). Future studies should elucidate the involvement of these AAs in the molecular pathway of IgE- and non-IgE-mediated allergic responses.
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Affiliation(s)
- Kacper Packi
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- AllerGen, Center of Personalized Medicine, 97-300 Piotrkow Trybunalski, Poland
| | - Joanna Matysiak
- Faculty of Health Sciences, Calisia University-Kalisz, 62-800 Kalisz, Poland
| | - Szymon Plewa
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | | | - Eliza Matuszewska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Natalia Rzetecka
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Anna Bręborowicz
- Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-572 Poznan, Poland
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-806 Poznan, Poland
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Jangjou A, Moqadas M, Mohsenian L, Kamyab H, Chelliapan S, Alshehery S, Ali MA, Dehbozorgi F, Yadav KK, Khorami M, Zarei Jelyani N. Awareness raising and dealing with methanol poisoning based on effective strategies. ENVIRONMENTAL RESEARCH 2023; 228:115886. [PMID: 37072082 DOI: 10.1016/j.envres.2023.115886] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023]
Abstract
Intoxication with methanol most commonly occurs as a consequence of ingesting, inhaling, or coming into contact with formulations that include methanol as a base. Clinical manifestations of methanol poisoning include suppression of the central nervous system, gastrointestinal symptoms, and decompensated metabolic acidosis, which is associated with impaired vision and either early or late blindness within 0.5-4 h after ingestion. After ingestion, methanol concentrations in the blood that are greater than 50 mg/dl should raise some concern. Ingested methanol is typically digested by alcohol dehydrogenase (ADH), and it is subsequently redistributed to the body's water to attain a volume distribution that is about equivalent to 0.77 L/kg. Moreover, it is removed from the body as its natural, unchanged parent molecules. Due to the fact that methanol poisoning is relatively uncommon but frequently involves a large number of victims at the same time, this type of incident occupies a special position in the field of clinical toxicology. The beginning of the COVID-19 pandemic has resulted in an increase in erroneous assumptions regarding the preventative capability of methanol in comparison to viral infection. More than 1000 Iranians fell ill, and more than 300 of them passed away in March of this year after they consumed methanol in the expectation that it would protect them from a new coronavirus. The Atlanta epidemic, which involved 323 individuals and resulted in the deaths of 41, is one example of mass poisoning. Another example is the Kristiansand outbreak, which involved 70 people and resulted in the deaths of three. In 2003, the AAPCC received reports of more than one thousand pediatric exposures. Since methanol poisoning is associated with high mortality rates, it is vital that the condition be addressed seriously and managed as quickly as feasible. The objective of this review was to raise awareness about the mechanism and metabolism of methanol toxicity, the introduction of therapeutic interventions such as gastrointestinal decontamination and methanol metabolism inhibition, the correction of metabolic disturbances, and the establishment of novel diagnostic/screening nanoparticle-based strategies for methanol poisoning such as the discovery of ADH inhibitors as well as the detection of the adulteration of alcoholic drinks by nanoparticles in order to prevent methanol poisoning. In conclusion, increasing warnings and knowledge about clinical manifestations, medical interventions, and novel strategies for methanol poisoning probably results in a decrease in the death load.
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Affiliation(s)
- Ali Jangjou
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Moqadas
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Mohsenian
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hesam Kamyab
- Faculty of Architecture and Urbanism, UTE University, Calle Rumipamba S/N and Bourgeois, Quito, Ecuador; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India; Process Systems Engineering Centre (PROSPECT), Faculty of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.
| | - Shreeshivadasan Chelliapan
- Engineering Department, Razak Faculty of Technology and Informatics, Universiti Teknologi Malaysia, Jln Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia.
| | - Sultan Alshehery
- Department of Mechanical Engineering King Khalid University, zip code - 62217, Saudi Arabia
| | - Mohammed Azam Ali
- Department of Mechanical Engineering King Khalid University, zip code - 62217, Saudi Arabia
| | - Farbod Dehbozorgi
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal, 462044, India; Environmental and Atmospheric Sciences Research Group, Scientific Research Center, Al-Ayen University, Thi-Qar, Nasiriyah, 64001, Iraq
| | - Masoud Khorami
- Department of Civil Engineering, Islamic Azad University, Central Tehran Branch, Tehran, Iran
| | - Najmeh Zarei Jelyani
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Wang KC, Lerche MH, Ardenkjær-Larsen JH, Jensen PR. Formate Metabolism in Shigella flexneri and Its Effect on HeLa Cells at Different Stages during the Infectious Process. Microbiol Spectr 2023; 11:e0063122. [PMID: 37042762 PMCID: PMC10269805 DOI: 10.1128/spectrum.00631-22] [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: 03/25/2022] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
Shigellosis caused by Shigella is one of the most important foodborne illnesses in global health, but little is known about the metabolic cross talk between this bacterial pathogen and its host cells during the different stages of the infection process. A detailed understanding of the metabolism can potentially lead to new drug targets remedying the pressing problem of antibiotic resistance. Here, we use stable isotope-resolved metabolomics as an unbiased and fast method to investigate how Shigella metabolizes 13C-glucose in three different environments: inside the host cells, adhering to the host cells, and alone in suspension. We find that especially formate metabolism by bacteria is sensitive to these different environments. The role of formate in pathogen metabolism is sparsely described in the literature compared to the roles of acetate and butyrate. However, its metabolic pathway is regarded as a potential drug target due to its production in microorganisms and its absence in humans. Our study provides new knowledge about the regulatory effect of formate. Bacterial metabolism of formate is pH dependent when studied alone in culture medium, whereas this effect is less pronounced when the bacteria adhere to the host cells. Once the bacteria are inside the host cells, we find that formate accumulation is reduced. Formate also affects the host cells resulting in a reduced infection rate. This was correlated to an increased immune response. Thus, intriguingly formate plays a double role in pathogenesis by increasing the virulence of Shigella and at the same time stimulating the immune response of the host. IMPORTANCE Bacterial infection is a pressing societal concern due to development of resistance toward known antibiotics. Central carbon metabolism has been suggested as a potential new target for drug development, but metabolic changes upon infection remain incompletely understood. Here, we used a cellular infection model to study how the bacterial pathogen Shigella adapts its metabolism depending on the environment starting from the extracellular medium until Shigella successfully invaded and proliferated inside host cells. The mixed-acid fermentation of Shigella was the major metabolic pathway during the infectious process, and the glucose-derived metabolite formate surprisingly played a divergent role in the pathogen and in the host cell. Our data show reduced infection rate when both host cells and bacteria were treated with formate, which correlated with an upregulated immune response in the host cells. The formate metabolism in Shigella thus potentially provides a route toward alternative treatment strategies for Shigella prevention.
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Affiliation(s)
- Ke-Chuan Wang
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mathilde Hauge Lerche
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jan Henrik Ardenkjær-Larsen
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pernille Rose Jensen
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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Zvi-Kedem T, Vintila S, Kleiner M, Tchernov D, Rubin-Blum M. Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels. ISME COMMUNICATIONS 2023; 3:48. [PMID: 37210404 PMCID: PMC10199937 DOI: 10.1038/s43705-023-00254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 04/25/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.
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Affiliation(s)
- Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel.
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Pratim Das P, Jyoti Kalita M, Jyoti Talukdar A, Mohd Khan F, Dutta K, Kalita S, Goswami N, Hazarika G, Samudrala G, Ghaznavi Idris M, Dutta S, Medhi S. Evaluation and analysis of novel germline variants in ethanol metabolism pathway genes predisposition to liver disease. Gene 2023; 873:147451. [PMID: 37150234 DOI: 10.1016/j.gene.2023.147451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
The pathogenetic events of liver disease are seemingly determined by factors linked to ethanol metabolism. The variations in genes encoding enzymes of the ethanol metabolic pathway can influence exposure to alcohol and thus may act as risk factors for the development of liver disease. The present study aimed to understand the genetic aspect of germline variations in ethanol metabolic pathway genes in two major categories of liver disease i.e. ALD and NAFLD. Targeted Re-sequencing was performed in the two disease categories along with healthy control followed by an assessment and evaluation of the variants in a case vs control manner. The pathogenicity prediction was evaluated using SIFT, PolyPhen, PROVEN, LRT, CADD, FATHMM, EIGEN, REVEL and VarSome, while MD simulation of a novel significant variant was performed using the GROMACS 5.1.4 package. The annotation of targeted re-sequencing results revealed 2172 variants in different locations of the genes. Upon recurrent assessment predominantly focusing on exonic missense variants from these genes of the alcohol metabolism pathway, the ALDH1L2 [c.337C>G, p.Pro113Ala, (rs199841702)] variant was found highly significant with comprehensive results. The amino acid substitution tool that predicted protein stability due to a point mutation showed a decrease in stability. The genotyping distribution of the identified novel variant in the population revealed that heterozygosity is significantly distributed in ALD patients. However, the predominant association between the inherited variant and the cause of developing disease needs further robust study.
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Affiliation(s)
- Partha Pratim Das
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Manash Jyoti Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Anjan Jyoti Talukdar
- Department of Medicine, Gauhati Medical College & Hospital, Guwahati, Assam-781032
| | - Faraz Mohd Khan
- School of Life sciences, Jawaharlal Nehru University, New Delhi, 110067
| | - Kalpajit Dutta
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Simanta Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Nabajyoti Goswami
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Gautam Hazarika
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | | | | | - Sangit Dutta
- Department of Medicine, Gauhati Medical College & Hospital, Guwahati, Assam-781032
| | - Subhash Medhi
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014.
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Green AC, Marttila P, Kiweler N, Chalkiadaki C, Wiita E, Cookson V, Lesur A, Eiden K, Bernardin F, Vallin KSA, Borhade S, Long M, Ghahe EK, Jiménez-Alonso JJ, Jemth AS, Loseva O, Mortusewicz O, Meyers M, Viry E, Johansson AI, Hodek O, Homan E, Bonagas N, Ramos L, Sandberg L, Frödin M, Moussay E, Slipicevic A, Letellier E, Paggetti J, Sørensen CS, Helleday T, Henriksson M, Meiser J. Formate overflow drives toxic folate trapping in MTHFD1 inhibited cancer cells. Nat Metab 2023; 5:642-659. [PMID: 37012496 PMCID: PMC10132981 DOI: 10.1038/s42255-023-00771-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023]
Abstract
Cancer cells fuel their increased need for nucleotide supply by upregulating one-carbon (1C) metabolism, including the enzymes methylenetetrahydrofolate dehydrogenase-cyclohydrolase 1 and 2 (MTHFD1 and MTHFD2). TH9619 is a potent inhibitor of dehydrogenase and cyclohydrolase activities in both MTHFD1 and MTHFD2, and selectively kills cancer cells. Here, we reveal that, in cells, TH9619 targets nuclear MTHFD2 but does not inhibit mitochondrial MTHFD2. Hence, overflow of formate from mitochondria continues in the presence of TH9619. TH9619 inhibits the activity of MTHFD1 occurring downstream of mitochondrial formate release, leading to the accumulation of 10-formyl-tetrahydrofolate, which we term a 'folate trap'. This results in thymidylate depletion and death of MTHFD2-expressing cancer cells. This previously uncharacterized folate trapping mechanism is exacerbated by physiological hypoxanthine levels that block the de novo purine synthesis pathway, and additionally prevent 10-formyl-tetrahydrofolate consumption for purine synthesis. The folate trapping mechanism described here for TH9619 differs from other MTHFD1/2 inhibitors and antifolates. Thus, our findings uncover an approach to attack cancer and reveal a regulatory mechanism in 1C metabolism.
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Affiliation(s)
- Alanna C Green
- Weston Park Cancer Centre and Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Petra Marttila
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Nicole Kiweler
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Christina Chalkiadaki
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Victoria Cookson
- Weston Park Cancer Centre and Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Antoine Lesur
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Kim Eiden
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - François Bernardin
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Karl S A Vallin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
- RISE Research Institutes of Sweden, Södertälje, Sweden
| | - Sanjay Borhade
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
- RedGlead Discover, Lund, Sweden
| | - Maeve Long
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Elahe Kamali Ghahe
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Julio J Jiménez-Alonso
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
- Department of Pharmacology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Marianne Meyers
- Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, Molecular Disease Mechanisms Group, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elodie Viry
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Annika I Johansson
- Swedish Metabolomics Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Ondřej Hodek
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Nadilly Bonagas
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Louise Ramos
- Weston Park Cancer Centre and Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Lars Sandberg
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Morten Frödin
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Etienne Moussay
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Ana Slipicevic
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
- One-carbon Therapeutics AB, Stockholm, Sweden
| | - Elisabeth Letellier
- Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, Molecular Disease Mechanisms Group, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jérôme Paggetti
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Thomas Helleday
- Weston Park Cancer Centre and Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK.
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Martin Henriksson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
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Yao Y, Fu B, Han D, Zhang Y, Wei Z, Liu H. Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:129-141. [PMID: 36779246 PMCID: PMC10103890 DOI: 10.1111/1758-2229.13129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/23/2022] [Indexed: 05/20/2023]
Abstract
Acetogens are anaerobes using Wood-Ljungdahl pathway (WLP) as the terminal electron acceptor for both assimilation and dissimilation of CO2 and widely distributed in diverse habitats. However, their habitat adaptation is often unclear. Given that bacterial genome evolution is often the result of environmental selective pressure, hereby we analysed gene copy number, phylogeny and selective pressure of genes involved in WLP within known genomes of 43 species to study the habitat adaption of gastrointestinal acetogens. The gene copy number of formate dehydrogenase (FDH) in gastrointestinal acetogens was much lower than that of non-gastrointestinal acetogens, and in five cases, no FDH genes were found in the genomes of five gastrointestinal acetogens, but that of the other WLP genes showed no difference. The evolutionary pattern of FDH genes was significantly different from that of the other enzymes. Additionally, seven positively selected sites were only identified in the fdhF genes, which means fdhF mutations favoured their adaptation. Collectively, reduction or loss of FDH genes and their evolutionary pattern as well as positive selection in gastrointestinal acetogens indicated their adaptation to formate-rich habitats, implying that FDH genes catalysing CO2 reduction to formate as the first step of methyl branch of WLP may have evolved independently.
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Affiliation(s)
- Ye Yao
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
| | - Dongfei Han
- School of Environmental Science and EngineeringSuzhou University of Science and TechnologySuzhouPeople's Republic of China
- Institute of Environment and Sustainable Development in AgricultureChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Zhang
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
| | - Zhiyuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of MedicineJiangnan UniversityWuxiJiangsuChina
| | - He Liu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
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38
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Weng C, Yang H, Loh BS, Wong MW, Ang WH. Targeting Pathogenic Formate-Dependent Bacteria with a Bioinspired Metallo-Nitroreductase Complex. J Am Chem Soc 2023; 145:6453-6461. [PMID: 36881731 DOI: 10.1021/jacs.3c00237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Nitroreductases (NTRs) constitute an important class of oxidoreductase enzymes that have evolved to metabolize nitro-containing compounds. Their unique characteristics have spurred an array of potential uses in medicinal chemistry, chemical biology, and bioengineering toward harnessing nitro caging groups and constructing NTR variants for niche applications. Inspired by how they carry out enzymatic reduction via a cascade of hydride transfer reactions, we sought to develop a synthetic small-molecule NTR system based on transfer hydrogenation mediated by transition metal complexes harnessing native cofactors. We report the first water-stable Ru-arene complex capable of selectively and fully reducing nitroaromatics into anilines in a biocompatible buffered aqueous environment using formate as the hydride source. We further demonstrated its application to activate nitro-caged sulfanilamide prodrug in formate-abundant bacteria, specifically pathogenic methicillin-resistant Staphylococcus aureus. This proof of concept paves the way for a new targeted antibacterial chemotherapeutic approach leveraging on redox-active metal complexes for prodrug activation via bioinspired nitroreduction.
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Affiliation(s)
- Cheng Weng
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
| | - Hui Yang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
| | - Boon Shing Loh
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
- NUS Graduate School─Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
- NUS Graduate School─Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
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39
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Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions. Metab Eng 2023; 76:120-132. [PMID: 36720400 DOI: 10.1016/j.ymben.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 12/13/2022] [Accepted: 01/21/2023] [Indexed: 01/29/2023]
Abstract
Multi-strain probiotics are widely regarded as effective products for improving gut microbiota stability and host health, providing advantages over single-strain probiotics. However, in general, it is unclear to what extent different strains would cooperate or compete for resources, and how the establishment of a common biofilm microenvironment could influence their interactions. In this work, we develop an integrative experimental and computational approach to comprehensively assess the metabolic functionality and interactions of probiotics across growth conditions. Our approach combines co-culture assays with genome-scale modelling of metabolism and multivariate data analysis, thus exploiting complementary data- and knowledge-driven systems biology techniques. To show the advantages of the proposed approach, we apply it to the study of the interactions between two widely used probiotic strains of Lactobacillus reuteri and Saccharomyces boulardii, characterising their production potential for compounds that can be beneficial to human health. Our results show that these strains can establish a mixed cooperative-antagonistic interaction best explained by competition for shared resources, with an increased individual exchange but an often decreased net production of amino acids and short-chain fatty acids. Overall, our work provides a strategy that can be used to explore microbial metabolic fingerprints of biotechnological interest, capable of capturing multifaceted equilibria even in simple microbial consortia.
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Lee J, Shin JA, Lee EM, Nam M, Park EM. Noggin-mediated effects on metabolite profiles of microglia and oligodendrocytes after ischemic insult. J Pharm Biomed Anal 2023; 224:115196. [PMID: 36529041 DOI: 10.1016/j.jpba.2022.115196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Recent studies show that shifts in energy metabolism in activated microglia are linked to their functions and immune responses in the ischemic brain. We previously reported that an antagonist of the bone morphogenetic protein, noggin, enhanced myelination in the ischemic brain during the chronic phase, and conditioned media (CM) from activated BV2 microglia treated with noggin after ischemia/reperfusion (I/R) increased the expression of myelin basic protein (MBP) in oligodendrocytes (MO3.13). To determine whether noggin induced changes in cell metabolism, metabolite profiles in BV2 and MO3.13 cells were analyzed by untargeted metabolomics using 1H nuclear magnetic resonance spectroscopy. Compared to vehicle-treated BV2 cells, noggin treatment (100 ng/mL for 3 h after I/R) suppressed the I/R-induced increase in intracellular glucose and lactate levels but increased extracellular levels of glucose and several amino acids. When MO3.13 cells were exposed to noggin CM from BV2 cells, most of the vehicle CM-induced changes in the levels of metabolites such as choline, formate, and intermediates of oxidative phosphorylation were reversed, while the glycerol level was markedly increased. An increase in glycerol level was also observed in the noggin-treated ischemic brain and was further supported by the expression of glycerol-3-phosphate dehydrogenase 1 (required for glycerol synthesis) in the cytoplasm of MBP-positive oligodendrocytes in the ischemic brains treated with noggin. These results suggest that noggin-induced changes in the metabolism of microglia provide a favorable environment for myelin synthesis in oligodendrocytes during the recovery phase after ischemic stroke.
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Affiliation(s)
- Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea.
| | - Jin A Shin
- Department of Pharmacology, College of Medicine, Ewha Womans University, Seoul 07084, Republic of Korea
| | - Eun-Mi Lee
- Department of Pharmacology, College of Medicine, Ewha Womans University, Seoul 07084, Republic of Korea
| | - Miso Nam
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea; Food Analysis Research Center, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Eun-Mi Park
- Department of Pharmacology, College of Medicine, Ewha Womans University, Seoul 07084, Republic of Korea.
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Caprara CDSC, Mathias TK, Santos MDFC, D’Oca MGM, D’Oca CDRM, Roselet F, Abreu PC, Ramos DF. Application of 1H HR-MAS NMR-Based Metabolite Fingerprinting of Marine Microalgae. Metabolites 2023; 13:metabo13020202. [PMID: 36837821 PMCID: PMC9965007 DOI: 10.3390/metabo13020202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Natural products from the marine environment as well as microalgae, have been known for the complexity of the metabolites they produce due to their adaptability to different environmental conditions, which has been an inexhaustible source of several bioactive properties, such as antioxidant, anti-tumor, and antimicrobial. This study aims to characterize the main metabolites of three species of microalgae (Nannochloropsis oceanica, Chaetoceros muelleri, and Conticribra weissflogii), which have important applications in the biofuel and nutrition industries, by 1H High-resolution magic angle spinning nuclear magnetic resonance (1H HR-MAS NMR), a method which is non-destructive, is highly reproducible, and requires minimal sample preparation. Even though the three species were found in the same ecosystem and a superior production of lipid compounds was observed, important differences were identified in relation to the production of specialized metabolites. These distinct properties favor the use of these compounds as leaders in the development of new bioactive compounds, especially against environmental, human, and animal pathogens (One Health), and demonstrate their potential in the development of alternatives for aquaculture.
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Affiliation(s)
| | - Tatiane Ksyvickas Mathias
- NMR Laboratory, NMR Center, Departamento de Química, Universidade Federal do Paraná, Curitiba 81530-900, PR, Brazil
| | - Maria de Fátima C. Santos
- NMR Laboratory, NMR Center, Departamento de Química, Universidade Federal do Paraná, Curitiba 81530-900, PR, Brazil
| | - Marcelo G. M. D’Oca
- NMR Laboratory, NMR Center, Departamento de Química, Universidade Federal do Paraná, Curitiba 81530-900, PR, Brazil
| | - Caroline Da R. M. D’Oca
- NMR Laboratory, NMR Center, Departamento de Química, Universidade Federal do Paraná, Curitiba 81530-900, PR, Brazil
| | - Fabio Roselet
- Laboratório de Produção de Microalgas (LPM), Instituto de Oceanografia, Universidade Federal do Rio Grande (FURG), Rio Grande 96210-030, RS, Brazil
| | - Paulo Cesar Abreu
- Laboratório de Produção de Microalgas (LPM), Instituto de Oceanografia, Universidade Federal do Rio Grande (FURG), Rio Grande 96210-030, RS, Brazil
| | - Daniela Fernandes Ramos
- Laboratório de Desenvolvimento de Novos Fármacos (LADEFA), Universidade Federal do Rio Grande (FURG), Rio Grande 96200-400, RS, Brazil
- Núcleo de Desenvolvimento de Novos Fármacos—NUDEFA, Rua General Osório, s/n°, Campus Saúde, 2° andar, Rio Grande 96200-400, RS, Brazil
- Correspondence: ; Tel.: +55-53-3237-4634
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Marhuenda-Egea FC, Narro-Serrano J, Shalabi-Benavent MJ, Álamo-Marzo JM, Amador-Prous C, Algado-Rabasa JT, Garijo-Saiz AM, Marco-Escoto M. A metabolic readout of the urine metabolome of COVID-19 patients. Metabolomics 2023; 19:7. [PMID: 36694097 PMCID: PMC9873393 DOI: 10.1007/s11306-023-01971-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Analysis of urine samples from COVID-19 patients by 1H NMR reveals important metabolic alterations due to SAR-CoV-2 infection. Previous studies have identified biomarkers in urine that reflect metabolic alterations in COVID-19 patients. We have used 1H NMR to better define these metabolic alterations since this technique allows us to obtain a broad profile of the metabolites present in urine. This technique offers the advantage that sample preparation is very simple and gives us very complete information on the metabolites present. To detect these alterations, we have compared urine samples from COVID-19 patients (n = 35) with healthy people (n = 18). We used unsupervised (Robust PCA) and supervised (PLS-LDA) multivariate analysis methods to evaluate the differences between the two groups: COVID-19 and healthy controls. The differences focus on a group of metabolites related to energy metabolism (glucose, ketone bodies, glycine, creatinine, and citrate) and other processes related to bacterial flora (TMAO and formic acid) and detoxification (hippuric acid). The alterations in the urinary metabolome shown in this work indicate that SARS-CoV-2 causes a metabolic change from a normal situation of glucose consumption towards a gluconeogenic situation and possible insulin resistance.
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Affiliation(s)
- F C Marhuenda-Egea
- Departamento de Agroquímica y Bioquímica, Universidad de Alicante, Alicante, Spain.
| | - J Narro-Serrano
- Departamento de Química Física, Universidad de Alicante, Alicante, Spain
| | | | - J M Álamo-Marzo
- Biochemical Laboratory, Hospital Marina Baixa, Villajoyosa, Spain
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43
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The ovine conceptus utilizes extracellular serine, glucose, and fructose to generate formate via the one carbon metabolism pathway. Amino Acids 2023; 55:125-137. [PMID: 36383272 DOI: 10.1007/s00726-022-03212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022]
Abstract
Highly proliferative cells rely on one carbon (1C) metabolism for production of formate required for synthesis of purines and thymidine for nucleic acid synthesis. This study was to determine if extracellular serine and/or glucose and fructose contribute the production of formate in ovine conceptuses. Suffolk ewes (n = 8) were synchronized to estrus, bred to fertile rams, and conceptuses were collected on Day 17 of gestation. Conceptuses were either snap frozen in liquid nitrogen (n = 3) or placed in culture in medium (n = 5) containing either: 1) 4 mM D-glucose + 2 mM [U-13C]serine; 2) 6 mM glycine + 4 mM D-glucose + 2 mM [U-13C]serine; 3) 4 mM D-fructose + 2 mM [U-13C]serine; 4) 6 mM glycine + 4 mM D-fructose + 2 mM [U-13C]serine; 5) 4 mM D-glucose + 4 mM D-fructose + 2 mM [U-13C]serine; or 6) 6 mM glycine + 4 mM D-glucose + 4 mM D-fructose + 2 mM [U-13C]serine. After 2 h incubation, conceptuses in their respective culture medium were homogenized and the supernatant analyzed for 12C- and 13C-formate by gas chromatography and amino acids by high performance liquid chromatography. Ovine conceptuses produced both 13C- and 12C-formate, indicating that the [U-13C]serine, glucose, and fructose were utilized to generate formate, respectively. Greater amounts of 12C-formate than 13C-formate were produced, indicating that the ovine conceptus utilized more glucose and fructose than serine to produce formate. This study is the first to demonstrate that both 1C metabolism and serinogenesis are active metabolic pathways in ovine conceptuses during the peri-implantation period of pregnancy, and that hexose sugars are the preferred substrate for generating formate required for nucleotide synthesis for proliferating trophectoderm cells.
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Cheng CT, Lai JM, Chang PMH, Hong YR, Huang CYF, Wang FS. Identifying essential genes in genome-scale metabolic models of consensus molecular subtypes of colorectal cancer. PLoS One 2023; 18:e0286032. [PMID: 37205704 DOI: 10.1371/journal.pone.0286032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023] Open
Abstract
Identifying essential targets in the genome-scale metabolic networks of cancer cells is a time-consuming process. The present study proposed a fuzzy hierarchical optimization framework for identifying essential genes, metabolites and reactions. On the basis of four objectives, the present study developed a framework for identifying essential targets that lead to cancer cell death and evaluating metabolic flux perturbations in normal cells that have been caused by cancer treatment. Through fuzzy set theory, a multiobjective optimization problem was converted into a trilevel maximizing decision-making (MDM) problem. We applied nested hybrid differential evolution to solve the trilevel MDM problem to identify essential targets in genome-scale metabolic models for five consensus molecular subtypes (CMSs) of colorectal cancer. We used various media to identify essential targets for each CMS and discovered that most targets affected all five CMSs and that some genes were CMS-specific. We obtained experimental data on the lethality of cancer cell lines from the DepMap database to validate the identified essential genes. The results reveal that most of the identified essential genes were compatible with the colorectal cancer cell lines obtained from DepMap and that these genes, with the exception of EBP, LSS, and SLC7A6, could generate a high level of cell death when knocked out. The identified essential genes were mostly involved in cholesterol biosynthesis, nucleotide metabolisms, and the glycerophospholipid biosynthetic pathway. The genes involved in the cholesterol biosynthetic pathway were also revealed to be determinable, if a cholesterol uptake reaction was not induced when the cells were in the culture medium. However, the genes involved in the cholesterol biosynthetic pathway became non-essential if such a reaction was induced. Furthermore, the essential gene CRLS1 was revealed as a medium-independent target for all CMSs.
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Affiliation(s)
- Chao-Ting Cheng
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Jin-Mei Lai
- Department of Life Science, College of Science and Engineering, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Peter Mu-Hsin Chang
- Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Ren Hong
- Department of Biochemistry and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chi-Ying F Huang
- Institute of Biopharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Feng-Sheng Wang
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
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Georgoulis I, Bock C, Lannig G, Pörtner HO, Feidantsis K, Giantsis IA, Sokolova IM, Michaelidis B. Metabolic remodeling caused by heat hardening in the Mediterranean mussel Mytilus galloprovincialis. J Exp Biol 2022; 225:285988. [PMID: 36426666 DOI: 10.1242/jeb.244795] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
Organisms can modify and increase their thermal tolerance faster and more efficiently after a brief exposure to sublethal thermal stress. This response is called 'heat hardening' as it leads to the generation of phenotypes with increased heat tolerance. The aim of this study was to investigate the impact of heat hardening on the metabolomic profile of Mytilus galloprovincialis in order to identify the associated adjustments of biochemical pathways that might benefit the mussels' thermal tolerance. Thus, mussels were exposed sequentially to two different phases (heat hardening and acclimation phases). To gain further insight into the possible mechanisms underlying the metabolic response of the heat-hardened M. galloprovincialis, metabolomics analysis was complemented by the estimation of mRNA expression of phosphoenolpyruvate carboxykinase (PEPCK), pyruvate kinase (PK) and alternative oxidase (AOX) implicated in the metabolic pathways of gluconeogenesis, glycolysis and redox homeostasis, respectively. Heat-hardened mussels showed evidence of higher activity of the tricarboxylic acid (TCA) cycle and diversification of upregulated metabolic pathways, possibly as a mechanism to increase ATP production and extend survival under heat stress. Moreover, formate and taurine accumulation provide an antioxidant and cytoprotective role in mussels during hypoxia and thermal stress. Overall, the metabolic responses in non-heat-hardened and heat-hardened mussels underline the upper thermal limits of M. galloprovincialis, set at 26°C, and are in accordance with the OCLTT concept. The ability of heat-hardened mussels to undergo a rapid gain and slow loss of heat tolerance may be an advantageous strategy for coping with intermittent and often extreme temperatures.
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Affiliation(s)
- Ioannis Georgoulis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Christian Bock
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research, Integrative Ecophysiology, Postfach 120161, D-27515 Bremerhaven, Germany
| | - Gisela Lannig
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research, Integrative Ecophysiology, Postfach 120161, D-27515 Bremerhaven, Germany
| | - Hans-O Pörtner
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research, Integrative Ecophysiology, Postfach 120161, D-27515 Bremerhaven, Germany
| | - Konstantinos Feidantsis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, GR-53100 Florina, Greece
| | - Inna M Sokolova
- Department of Marine Biology, Institute of Biological Sciences, University of Rostock, D-18055 Rostock, Germany
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
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Melvin SD, Chaousis S, Finlayson K, Carroll AR, van de Merwe JP. Field-scale monitoring of green sea turtles (Chelonia mydas): Influence of site characteristics and capture technique on the blood metabolome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101026. [PMID: 36191476 DOI: 10.1016/j.cbd.2022.101026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 01/27/2023]
Abstract
Given their threatened status, there is considerable interest in establishing monitoring techniques that can be used to evaluate the health of sea turtles in the wild. The present study represents a methodological contribution towards field-scale metabolomic assessment of sea turtles, by exploring differences in blood biochemistry associated with site characteristics and capture technique. We compared the metabolome of blood from animals at three locations (two coastal and one reefal), collected from turtles that were either resting or active, and sampled across multiple seasons at one location. Our results show clear differences in the metabolome of turtles from the three locations, some of which are likely attributable to differences in diet or forage quality and others which may reflect differences in other factors (e.g., occurrence of land-based contaminants or other biotic and/or abiotic stressors) between coastal and reefal sites. Our analysis also revealed the influence of capture technique on metabolite profiles, with numerous markers of physical exertion in animals captured while active that were absent in turtles sampled while resting. We observed a modest potential for temporal differences in the metabolome, but controlling for sampling time did not change the overall conclusions of our study. This suggests that temporal differences in the metabolome warrant consideration when designing studies to evaluate the status of sea turtles in the wild, but that site characteristics and capture technique are bigger drivers. However, sample size for this comparison was relatively small and further investigation of seasonal differences in the metabolome are warranted. Research exploring each of these factors more closely will further contribute towards achieving robust metabolomics analysis of sea turtles across large spatial and temporal scales.
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Affiliation(s)
- Steven D Melvin
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia.
| | - Stephanie Chaousis
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia
| | - Kimberly Finlayson
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia
| | - Anthony R Carroll
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Southport, QLD, Australia
| | - Jason P van de Merwe
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia. https://twitter.com/@DrVanders
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Miller AW, Penniston KL, Fitzpatrick K, Agudelo J, Tasian G, Lange D. Mechanisms of the intestinal and urinary microbiome in kidney stone disease. Nat Rev Urol 2022; 19:695-707. [PMID: 36127409 PMCID: PMC11234243 DOI: 10.1038/s41585-022-00647-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2022] [Indexed: 02/08/2023]
Abstract
Kidney stone disease affects ~10% of the global population and the incidence continues to rise owing to the associated global increase in the incidence of medical conditions associated with kidney stone disease including, for example, those comprising the metabolic syndrome. Considering that the intestinal microbiome has a substantial influence on host metabolism, that evidence has suggested that the intestinal microbiome might have a role in maintaining oxalate homeostasis and kidney stone disease is unsurprising. In addition, the discovery that urine is not sterile but, like other sites of the human body, harbours commensal bacterial species that collectively form a urinary microbiome, is an additional factor that might influence the induction of crystal formation and stone growth directly in the kidney. Collectively, the microbiomes of the host could influence kidney stone disease at multiple levels, including intestinal oxalate absorption and direct crystal formation in the kidneys.
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Affiliation(s)
- Aaron W Miller
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Kristina L Penniston
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kate Fitzpatrick
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - José Agudelo
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gregory Tasian
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dirk Lange
- The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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Role of Staphylococcus aureus Formate Metabolism during Prosthetic Joint Infection. Infect Immun 2022; 90:e0042822. [PMID: 36286525 PMCID: PMC9670962 DOI: 10.1128/iai.00428-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms are bacterial communities characterized by antibiotic tolerance.
Staphylococcus aureus
is a leading cause of biofilm infections on medical devices, including prosthetic joints, which represent a significant health care burden. The major leukocyte infiltrate associated with
S. aureus
prosthetic joint infection (PJI) is granulocytic myeloid-derived suppressor cells (G-MDSCs), which produce IL-10 to promote biofilm persistence by inhibiting monocyte and macrophage proinflammatory activity.
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Metabolomics by NMR Combined with Machine Learning to Predict Neoadjuvant Chemotherapy Response for Breast Cancer. Cancers (Basel) 2022; 14:cancers14205055. [PMID: 36291837 PMCID: PMC9600495 DOI: 10.3390/cancers14205055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Neoadjuvant chemotherapy (NACT) is offered to breast cancer (BC) patients to downstage the disease. However, some patients may not respond to NACT, being resistant. We used the serum metabolic profile by Nuclear Magnetic Resonance (NMR) combined with disease characteristics to differentiate between sensitive and resistant BC patients. We obtained accuracy above 80% for the response prediction and showcased how NMR can substantially enhance the prediction of response to NACT. Abstract Neoadjuvant chemotherapy (NACT) is offered to patients with operable or inoperable breast cancer (BC) to downstage the disease. Clinical responses to NACT may vary depending on a few known clinical and biological features, but the diversity of responses to NACT is not fully understood. In this study, 80 women had their metabolite profiles of pre-treatment sera analyzed for potential NACT response biomarker candidates in combination with immunohistochemical parameters using Nuclear Magnetic Resonance (NMR). Sixty-four percent of the patients were resistant to chemotherapy. NMR, hormonal receptors (HR), human epidermal growth factor receptor 2 (HER2), and the nuclear protein Ki67 were combined through machine learning (ML) to predict the response to NACT. Metabolites such as leucine, formate, valine, and proline, along with hormone receptor status, were discriminants of response to NACT. The glyoxylate and dicarboxylate metabolism was found to be involved in the resistance to NACT. We obtained an accuracy in excess of 80% for the prediction of response to NACT combining metabolomic and tumor profile data. Our results suggest that NMR data can substantially enhance the prediction of response to NACT when used in combination with already known response prediction factors.
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50
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Zhou Q, Zhang F, Kerbl-Knapp J, Korbelius M, Kuentzel KB, Vujić N, Akhmetshina A, Hörl G, Paar M, Steyrer E, Kratky D, Madl T. Phosphatidylethanolamine N-Methyltransferase Knockout Modulates Metabolic Changes in Aging Mice. Biomolecules 2022; 12:1270. [PMID: 36139111 PMCID: PMC9496051 DOI: 10.3390/biom12091270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/11/2022] Open
Abstract
Phospholipid metabolism, including phosphatidylcholine (PC) biosynthesis, is crucial for various biological functions and is associated with longevity. Phosphatidylethanolamine N-methyltransferase (PEMT) is a protein that catalyzes the biosynthesis of PC, the levels of which change in various organs such as the brain and kidneys during aging. However, the role of PEMT for systemic PC supply is not fully understood. To address how PEMT affects aging-associated energy metabolism in tissues responsible for nutrient absorption, lipid storage, and energy consumption, we employed NMR-based metabolomics to study the liver, plasma, intestine (duodenum, jejunum, and ileum), brown/white adipose tissues (BAT and WAT), and skeletal muscle of young (9-10 weeks) and old (91-132 weeks) wild-type (WT) and PEMT knockout (KO) mice. We found that the effect of PEMT-knockout was tissue-specific and age-dependent. A deficiency of PEMT affected the metabolome of all tissues examined, among which the metabolome of BAT from both young and aged KO mice was dramatically changed in comparison to the WT mice, whereas the metabolome of the jejunum was only slightly affected. As for aging, the absence of PEMT increased the divergence of the metabolome during the aging of the liver, WAT, duodenum, and ileum and decreased the impact on skeletal muscle. Overall, our results suggest that PEMT plays a previously underexplored, critical role in both aging and energy metabolism.
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Affiliation(s)
- Qishun Zhou
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Fangrong Zhang
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
- Key Laboratory of Gastrointestinal Cancer, Fujian Medical University, Ministry of Education, Fuzhou 350122, China
| | - Jakob Kerbl-Knapp
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Melanie Korbelius
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Katharina Barbara Kuentzel
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Nemanja Vujić
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Alena Akhmetshina
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Gerd Hörl
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Margret Paar
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Ernst Steyrer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Tobias Madl
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
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