1
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Tang Q, Tillmann M, Cohen JD. Analytical methods for stable isotope labeling to elucidate rapid auxin kinetics in Arabidopsis thaliana. PLoS One 2024; 19:e0303992. [PMID: 38776314 PMCID: PMC11111016 DOI: 10.1371/journal.pone.0303992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024] Open
Abstract
The phytohormone auxin plays a critical role in plant growth and development. Despite significant progress in elucidating metabolic pathways of the primary bioactive auxin, indole-3-acetic acid (IAA), over the past few decades, key components such as intermediates and enzymes have not been fully characterized, and the dynamic regulation of IAA metabolism in response to environmental signals has not been completely revealed. In this study, we established a protocol employing a highly sensitive liquid chromatography-mass spectrometry (LC-MS) instrumentation and a rapid stable isotope labeling approach. We treated Arabidopsis seedlings with two stable isotope labeled precursors ([13C6]anthranilate and [13C8, 15N1]indole) and monitored the label incorporation into proposed indolic compounds involved in IAA biosynthetic pathways. This Stable Isotope Labeled Kinetics (SILK) method allowed us to trace the turnover rates of IAA pathway precursors and product concurrently with a time scale of seconds to minutes. By measuring the entire pathways over time and using different isotopic tracer techniques, we demonstrated that these methods offer more detailed information about this complex interacting network of IAA biosynthesis, and should prove to be useful for studying auxin metabolic network in vivo in a variety of plant tissues and under different environmental conditions.
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Affiliation(s)
- Qian Tang
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jerry D. Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
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2
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Meiser J, Frezza C. Presenting metabolomics analyses: what's in a number? EMBO J 2024:10.1038/s44318-024-00098-1. [PMID: 38664540 DOI: 10.1038/s44318-024-00098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/09/2024] Open
Affiliation(s)
- Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Christian Frezza
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University Hospital Cologne, Cologne, Germany.
- Institute of Genetics, Faculty of Mathematics and Natural Sciences, Faculty of Medicine, University of Cologne, Cologne, Germany.
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3
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Pignataro E, Pini F, Barbanente A, Arnesano F, Palazzo A, Marsano RM. Flying toward a plastic-free world: Can Drosophila serve as a model organism to develop new strategies of plastic waste management? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169942. [PMID: 38199375 DOI: 10.1016/j.scitotenv.2024.169942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
The last century was dominated by the widespread use of plastics, both in terms of invention and increased usage. The environmental challenge we currently face is not just about reducing plastic usage but finding new ways to manage plastic waste. Recycling is growing but remains a small part of the solution. There is increasing focus on studying organisms and processes that can break down plastics, offering a modern approach to addressing the environmental crisis. Here, we provide an overview of the organisms associated with plastics biodegradation, and we explore the potential of harnessing and integrating their genetic and biochemical features into a single organism, such as Drosophila melanogaster. The remarkable genetic engineering and microbiota manipulation tools available for this organism suggest that multiple features could be amalgamated and modeled in the fruit fly. We outline feasible genetic engineering and gut microbiome engraftment strategies to develop a new class of plastic-degrading organisms and discuss of both the potential benefits and the limitations of developing such engineered Drosophila melanogaster strains.
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Affiliation(s)
- Eugenia Pignataro
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
| | - Francesco Pini
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
| | - Alessandra Barbanente
- Department of Chemistry, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.
| | - Fabio Arnesano
- Department of Chemistry, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.
| | - Antonio Palazzo
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
| | - René Massimiliano Marsano
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
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4
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Riscal R, Riquier-Morcant B, Gadea G, Linares LK. Give and Take: The Reciprocal Control of Metabolism and Cell Cycle. Methods Mol Biol 2024; 2740:155-168. [PMID: 38393475 DOI: 10.1007/978-1-0716-3557-5_10] [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] [Indexed: 02/25/2024]
Abstract
Cell cycle is an ordered sequence of events that occur in a cell preparing for cell division . The cell cycle is a four-stage process in which the cell increases in size, copies its DNA , prepares to divide, and divides. All these stages require a coordination of signaling pathways as well as adequate levels of energy and building blocks. These specific signaling and metabolic switches are tightly orchestrated in order for the cell cycle to occur properly. In this book chapter, we will provide information on the basis of metabolism and cell cycle interplay, and we will finish by an unexhaustive list of metabolomics approaches available to study the reciprocal control of metabolism and cell cycle.
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Affiliation(s)
- Romain Riscal
- INSERM U1194, IRCM, Institut de Recherche en Cancérologie de Montpellier, Institut régional du Cancer de Montpellier, Université de Montpellier, Montpellier, France
| | - Blanche Riquier-Morcant
- INSERM U1194, IRCM, Institut de Recherche en Cancérologie de Montpellier, Institut régional du Cancer de Montpellier, Université de Montpellier, Montpellier, France
| | - Gilles Gadea
- INSERM U1194, IRCM, Institut de Recherche en Cancérologie de Montpellier, Institut régional du Cancer de Montpellier, Université de Montpellier, Montpellier, France
| | - Laetitia K Linares
- INSERM U1194, IRCM, Institut de Recherche en Cancérologie de Montpellier, Institut régional du Cancer de Montpellier, Université de Montpellier, Montpellier, France.
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5
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Sun Y, Tang H, Du S, Chen Y, Ou Z, Zhang M, Chen Z, Tang Z, Zhang D, Chen T, Xu Y, Li J, Norback D, Hashim JH, Hashim Z, Shao J, Fu X, Zhao Z. Indoor metabolites and chemicals outperform microbiome in classifying childhood asthma and allergic rhinitis. ECO-ENVIRONMENT & HEALTH (ONLINE) 2023; 2:208-218. [PMID: 38435359 PMCID: PMC10902507 DOI: 10.1016/j.eehl.2023.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 03/05/2024]
Abstract
Indoor microorganisms impact asthma and allergic rhinitis (AR), but the associated microbial taxa often vary extensively due to climate and geographical variations. To provide more consistent environmental assessments, new perspectives on microbial exposure for asthma and AR are needed. Home dust from 97 cases (32 asthma alone, 37 AR alone, 28 comorbidity) and 52 age- and gender-matched controls in Shanghai, China, were analyzed using high-throughput shotgun metagenomic sequencing and liquid chromatography-mass spectrometry. Homes of healthy children were enriched with environmental microbes, including Paracoccus, Pseudomonas, and Psychrobacter, and metabolites like keto acids, indoles, pyridines, and flavonoids (astragalin, hesperidin) (False Discovery Rate < 0.05). A neural network co-occurrence probability analysis revealed that environmental microorganisms were involved in producing these keto acids, indoles, and pyridines. Conversely, homes of diseased children were enriched with mycotoxins and synthetic chemicals, including herbicides, insecticides, and food/cosmetic additives. Using a random forest model, characteristic metabolites and microorganisms in Shanghai homes were used to classify high and low prevalence of asthma/AR in an independent dataset in Malaysian schools (N = 1290). Indoor metabolites achieved an average accuracy of 74.9% and 77.1% in differentiating schools with high and low prevalence of asthma and AR, respectively, whereas indoor microorganisms only achieved 51.0% and 59.5%, respectively. These results suggest that indoor metabolites and chemicals rather than indoor microbiome are potentially superior environmental indicators for childhood asthma and AR. This study extends the traditional risk assessment focusing on allergens or air pollutants in childhood asthma and AR, thereby revealing potential novel intervention strategies for these diseases.
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Affiliation(s)
- Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hao Tang
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Shuang Du
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhuoru Chen
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Zhiwei Tang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dongjun Zhang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tianyi Chen
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Yanyi Xu
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Jiufeng Li
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Dan Norback
- Department of Medical Sciences, Uppsala University, Uppsala SE-751, Sweden
| | - Jamal Hisham Hashim
- Department of Environmental Health, Faculty of Health Sciences, Universiti Selangor, Shah Alam 40000, Malaysia
| | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Malaysia
| | - Jie Shao
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhuohui Zhao
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
- Key Laboratory of Public Health Safety of the Ministry of Education, Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai 200030, China
- IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan University, Shanghai 200438, China
- WMO/IGAC MAP-AQ Asian Office Shanghai, Fudan University, Shanghai 200438, China
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6
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Straub M, Auderset A, de Leval L, Piazzon N, Maison D, Vozenin MC, Ollivier J, Petit B, Sigman DM, Martínez-García A. Nitrogen isotopic composition as a gauge of tumor cell anabolism-to-catabolism ratio. Sci Rep 2023; 13:19796. [PMID: 37957187 PMCID: PMC10643536 DOI: 10.1038/s41598-023-45597-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Studies have suggested that cancerous tissue has a lower 15N/14N ratio than benign tissue. However, human data have been inconclusive, possibly due to constraints on experimental design. Here, we used high-sensitivity nitrogen isotope methods to assess the 15N/14N ratio of human breast, lung, and kidney cancer tissue at unprecedented spatial resolution. In lung, breast, and urothelial carcinoma, 15N/14N was negatively correlated with tumor cell density. The magnitude of 15N depletion for a given tumor cell density was consistent across different types of lung cancer, ductal in situ and invasive breast carcinoma, and urothelial carcinoma, suggesting similar elevations in the anabolism-to-catabolism ratio. However, tumor 15N depletion was higher in a more aggressive metaplastic breast carcinoma. These findings may indicate the ability of certain cancers to more effectively channel N towards growth. Our results support 15N/14N analysis as a potential tool for screening biopsies and assessing N metabolism in tumor cells.
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Affiliation(s)
- Marietta Straub
- Institute of Radiation Physics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
- Max Planck Institute for Chemistry, 55128, Mainz, Germany.
| | - Alexandra Auderset
- Max Planck Institute for Chemistry, 55128, Mainz, Germany
- School of Ocean and Earth Science, University of Southampton, Southampton, SO14 3ZH, UK
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nathalie Piazzon
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Damien Maison
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Marie-Catherine Vozenin
- Radiation Oncology Laboratory/DO/Radio-Oncology/CHUV, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jonathan Ollivier
- Radiation Oncology Laboratory/DO/Radio-Oncology/CHUV, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Benoît Petit
- Radiation Oncology Laboratory/DO/Radio-Oncology/CHUV, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Daniel M Sigman
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
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7
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Whitby A, Pabla P, Shastri B, Amugi L, Del Río-Álvarez Á, Kim DH, Royo L, Armengol C, Dandapani M. Characterisation of Aberrant Metabolic Pathways in Hepatoblastoma Using Liquid Chromatography and Tandem Mass Spectrometry (LC-MS/MS). Cancers (Basel) 2023; 15:5182. [PMID: 37958356 PMCID: PMC10648437 DOI: 10.3390/cancers15215182] [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: 08/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Hepatoblastoma (HB) is a rare childhood tumour with an evolving molecular landscape. We present the first comprehensive metabolomic analysis using untargeted and targeted liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS) of paired tumour and non-tumour surgical samples in HB patients (n = 8 pairs). This study demonstrates that the metabolomic landscape of HB is distinct from that of non-tumour (NT) liver tissue, with 35 differentially abundant metabolites mapping onto pathways such as fatty acid transport, glycolysis, the tricarboxylic acid (TCA) cycle, branched-chain amino acid degradation and glutathione synthesis. Targeted metabolomics demonstrated reduced short-chain acylcarnitines and a relative accumulation of branched-chain amino acids. Medium- and long-chain acylcarnitines in HB were similar to those in NT. The metabolomic changes reported are consistent with previously reported transcriptomic data from tumour and non-tumour samples (49 out of 54 targets) as well as metabolomic data obtained using other techniques. Gene set enrichment analysis (GSEA) from RNAseq data (n = 32 paired HB and NT samples) demonstrated a downregulation of the carnitine metabolome and immunohistochemistry showed a reduction in CPT1a (n = 15 pairs), which transports fatty acids into the mitochondria, suggesting a lack of utilisation of long-chain fatty acids in HB. Thus, our findings suggest a reduced metabolic flux in HB which is corroborated at the gene expression and protein levels. Further work could yield novel insights and new therapeutic targets.
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Affiliation(s)
- Alison Whitby
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Pardeep Pabla
- School of Medicine, Royal Derby Hospital Centre, University of Nottingham, Derby DE22 3DT, UK
| | - Bhoomi Shastri
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laudina Amugi
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Álvaro Del Río-Álvarez
- Childhood Liver Oncology Group, Translational Program in Cancer Research (CARE), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) en Enfermedades Hepáticas y Digestivas, 28029 Madrid, Spain
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Royo
- Childhood Liver Oncology Group, Translational Program in Cancer Research (CARE), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
| | - Carolina Armengol
- Childhood Liver Oncology Group, Translational Program in Cancer Research (CARE), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) en Enfermedades Hepáticas y Digestivas, 28029 Madrid, Spain
| | - Madhumita Dandapani
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
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8
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Jin Y, Chi J, LoMonaco K, Boon A, Gu H. Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome. Trends Analyt Chem 2023; 166:117155. [PMID: 37484879 PMCID: PMC10361410 DOI: 10.1016/j.trac.2023.117155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.
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Affiliation(s)
- Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jinhua Chi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Kaelene LoMonaco
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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9
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Vera-Siguenza E, Escribano-Gonzalez C, Serrano-Gonzalo I, Eskla KL, Spill F, Tennant D. Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model. PLoS Comput Biol 2023; 19:e1011374. [PMID: 37713666 PMCID: PMC10503963 DOI: 10.1371/journal.pcbi.1011374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 07/19/2023] [Indexed: 09/17/2023] Open
Abstract
It is increasingly apparent that cancer cells, in addition to remodelling their metabolism to survive and proliferate, adapt and manipulate the metabolism of other cells. This property may be a telling sign that pre-clinical tumour metabolism studies exclusively utilising in-vitro mono-culture models could prove to be limited for uncovering novel metabolic targets able to translate into clinical therapies. Although this is increasingly recognised, and work towards addressing the issue is becoming routinary much remains poorly understood. For instance, knowledge regarding the biochemical mechanisms through which cancer cells manipulate non-cancerous cell metabolism, and the subsequent impact on their survival and proliferation remains limited. Additionally, the variations in these processes across different cancer types and progression stages, and their implications for therapy, also remain largely unexplored. This study employs an interdisciplinary approach that leverages the predictive power of mathematical modelling to enrich experimental findings. We develop a functional multicellular in-silico model that facilitates the qualitative and quantitative analysis of the metabolic network spawned by an in-vitro co-culture model of bone marrow mesenchymal stem- and myeloma cell lines. To procure this model, we devised a bespoke human genome constraint-based reconstruction workflow that combines aspects from the legacy mCADRE & Metabotools algorithms, the novel redHuman algorithm, along with 13C-metabolic flux analysis. Our workflow transforms the latest human metabolic network matrix (Recon3D) into two cell-specific models coupled with a metabolic network spanning a shared growth medium. When cross-validating our in-silico model against the in-vitro model, we found that the in-silico model successfully reproduces vital metabolic behaviours of its in-vitro counterpart; results include cell growth predictions, respiration rates, as well as support for observations which suggest cross-shuttling of redox-active metabolites between cells.
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Affiliation(s)
- Elias Vera-Siguenza
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Watson School of Mathematics, University of Birmingham, Birmingham, United Kingdom
| | - Cristina Escribano-Gonzalez
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Irene Serrano-Gonzalo
- Instituto de Investigación Sanitaria Aragón, Fundación Española para el Estudio y Terapéutica de la enfermedad de Gaucher y otras Lisosomales, Zaragoza, España
| | - Kattri-Liis Eskla
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Fabian Spill
- Watson School of Mathematics, University of Birmingham, Birmingham, United Kingdom
| | - Daniel Tennant
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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10
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Gumieniczek A, Berecka-Rycerz A. Metabolism and Chemical Degradation of New Antidiabetic Drugs: A Review of Analytical Approaches for Analysis of Glutides and Gliflozins. Biomedicines 2023; 11:2127. [PMID: 37626624 PMCID: PMC10452759 DOI: 10.3390/biomedicines11082127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
The drug metabolism and drug degradation pathways may overlap, resulting in the formation of similar constituents. Therefore, the metabolism data can be helpful for deriving safe levels of degradation impurities and improving the quality of respective pharmaceutical products. The present article contains considerations on possible links between metabolic and degradation pathways for new antidiabetic drugs such as glutides, gliflozins, and gliptins. Special attention was paid to their reported metabolites and identified degradation products. At the same time, many interesting analytical approaches to conducting metabolism as well as degradation experiments were mentioned, including chromatographic methods and radioactive labeling of the drugs. The review addresses the analytical approaches elaborated for examining the metabolism and degradation pathways of glutides, i.e., glucagon like peptide 1 (GLP-1) receptor agonists, and gliflozins, i.e., sodium glucose co-transporter 2 (SGLT2) inhibitors. The problems associated with the chromatographic analysis of the peptide compounds (glutides) and the polar drugs (gliflozins) were addressed. Furthermore, issues related to in vitro experiments and the use of stable isotopes were discussed.
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Affiliation(s)
- Anna Gumieniczek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 4, 20-090 Lublin, Poland;
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11
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Xia W, Fang X, Gao Y, Wu W, Han Y, Liu R, Yang H, Chen H, Gao H. Advances of stable isotope technology in food safety analysis and nutrient metabolism research. Food Chem 2023; 408:135191. [PMID: 36527919 DOI: 10.1016/j.foodchem.2022.135191] [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: 08/27/2022] [Revised: 11/21/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Food quality, safety, and the regulatory metabolism of food nutrients in cells are primary factors in determining human health. However, residues of undesirable or hazardous compounds in food products and dysregulation in the nutrient metabolism inevitably occur occasionally. For years, chromatography-mass spectrometry technology has been recognized as an essential research tool in food analysis and nutrient metabolism research, and it is more accurate and robust when coupled with stable isotopes. In this study, we summarize the applications of stable isotope technology in the quantification of contaminant residues (pesticides, veterinary drugs, mycotoxins, polycyclic aromatic hydrocarbons, and other hazardous compounds) in foods and in the nutrients (glucose, lipids, amino acids and proteins) metabolism research. The aim of this review was to serve as a reference for providing effective analysis techniques for protecting food quality and human health, and to pave the way for the broader application of stable isotope technology.
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Affiliation(s)
- Wei Xia
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Xiangjun Fang
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Yuan Gao
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Weijie Wu
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Yanchao Han
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Ruiling Liu
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Hailong Yang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China.
| | - Hangjun Chen
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China.
| | - Haiyan Gao
- Key Laboratory of Post-Harvest Handing of Fruits, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China.
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Morgan KD. The use of nitrogen-15 in microbial natural product discovery and biosynthetic characterization. Front Microbiol 2023; 14:1174591. [PMID: 37234518 PMCID: PMC10206073 DOI: 10.3389/fmicb.2023.1174591] [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: 02/26/2023] [Accepted: 04/17/2023] [Indexed: 05/28/2023] Open
Abstract
This mini-review covers the use of nitrogen-15 in bacterial and fungal natural product discovery and biosynthetic characterization from 1970 to 2022. Nitrogen is an important element in a number of bioactive and structurally intriguing natural products including alkaloids, non-ribosomal peptides, and hybrid natural products. Nitrogen-15 can be detected at natural abundance utilizing two-dimensional nuclear magnetic resonance and mass spectrometry. Additionally, it is a stable isotope that can be added to growth media for both filamentous fungi and bacteria. With stable isotope feeding, additional two-dimensional nuclear magnetic resonance and mass spectrometry strategies have become available, and there is a growing trend to use nitrogen-15 stable isotope feeding for the biosynthetic characterization of natural products. This mini-review will catalog the use of these strategies, analyze the strengths and weaknesses of the different approaches, and suggest future directions for the use of nitrogen-15 in natural product discovery and biosynthetic characterization.
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Kumar S, Gajjela R, Kumar H, Arulraj RA, Subramaniam S, Kothandaramachandran T, Sudhir V S, Chauthe SK, Gupta A, Mathur A, Roy A, Bagadi M, Caceres-Cortes J. A strategy for evaluation of isotopic enrichment and structural integrity of deuterium labelled compounds by using HR-MS and NMR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1470-1477. [PMID: 36876453 DOI: 10.1039/d2ay01980a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Determining the purity of deuterium labelled compounds is important due to the increasing use of these compounds in mass spectrometry (MS) based quantitative analyses for targeting metabolic flux, reducing toxicity, confirming reaction mechanisms during synthesis, predicting enzyme mechanisms, and enhancing the efficacy of drugs, in quantitative proteomics, and also as internal standards. In the present study, a strategy using liquid chromatography electrospray ionization high resolution mass spectrometry (LC-ESI-HR-MS) and nuclear magnetic resonance (NMR) spectroscopy was proposed to determine the isotopic enrichment and structural integrity of deuterium labelled compounds. The proposed strategy involves recording full scan MS, extracting and integrating isotopic ions, and calculating the isotopic enrichment of the desired labelled compounds. NMR analysis confirms structural integrity or positions of labelled atoms and can provide insights into the relative percent isotopic purity. This strategy was used to evaluate the isotopic enrichment and structural integrity of in-house synthesized compounds as well as a series of commercially available deuterium labelled compounds. The % isotopic purity for labelled compounds of a benzofuranone derivative (BEN-d2), tamsulosin-d4 (TAM-d4), oxybutynin-d5 (OXY-d5), eplerenone-d3 (EPL-d3), and propafenone-d7 (PRO-d7) was calculated and found to be 94.7, 99.5, 98.8, 99.9, and 96.5, respectively. All the samples were run in triplicate and the results were observed to be reproducible.
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Affiliation(s)
- Sumit Kumar
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Raju Gajjela
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Hemantha Kumar
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Ruba A Arulraj
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Srinath Subramaniam
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Bangalore, India
| | | | - Sai Sudhir V
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Bangalore, India
| | - Siddheshwar Kisan Chauthe
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Anuradha Gupta
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Bangalore, India
| | - Arvind Mathur
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol Myers Squibb Research and Development, P.O. Box 5400, Princeton, New Jersey 08543-4000, USA
| | - Amrita Roy
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Muralidhararao Bagadi
- Discovery Analytical Sciences, Biocon Bristol Myers Squibb Research & Development Center (BBRC), Syngene International Ltd, Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India - 560 099.
| | - Janet Caceres-Cortes
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol Myers Squibb Research and Development, P.O. Box 5400, Princeton, New Jersey 08543-4000, USA
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14
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Wu X, Chen W, Holmberg-Douglas N, Bida GT, Tu X, Ma X, Wu Z, Nicewicz DA, Li Z. 11C, 12C and 13C-Cyanation of Electron-Rich Arenes via Organic Photoredox Catalysis. Chem 2023; 9:343-362. [PMID: 36777049 PMCID: PMC9913897 DOI: 10.1016/j.chempr.2022.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a non-invasive imaging technology, positron emission tomography (PET) plays a crucial role in personalized medicine, including early diagnosis, patient screening, and treatment monitoring. The advancement of PET research depends on the discovery of new PET agents, which requires the development of simple and efficient radiolabeling methods in many cases. As bioisosteres for halogen and carbonyl moieties, nitriles are important functional groups in pharmaceutical and agrochemical compounds. Here, we disclose a mild organophotoredox-catalyzed method for efficient cyanation of a broad spectrum of electron-rich arenes, including abundant and readily available veratroles and pyrogallol trimethyl ethers. Notably, the transformations not only are compatible with various affordable 12C and 13C-cyanide sources, but also could be applied to carbon-11 synthons to incorporate [11C]nitriles into arenes. The aryl [11C]nitriles can be further derivatized to [11C]carboxylic acids, [11C]amides, and [11C]alkyl amines. The newly developed reaction can serve as a powerful tool for generating new PET agents.
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Affiliation(s)
- Xuedan Wu
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Wei Chen
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Natalie Holmberg-Douglas
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-3290, United States
| | - Gerald Thomas Bida
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Xianshuang Tu
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Xinrui Ma
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Zhanhong Wu
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - David A. Nicewicz
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-3290, United States
| | - Zibo Li
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
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15
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Ahmad F, Nadeem H. Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery. Methods Mol Biol 2023; 2575:77-103. [PMID: 36301472 DOI: 10.1007/978-1-0716-2716-7_5] [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] [Indexed: 06/16/2023]
Abstract
The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.
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Affiliation(s)
- Faheem Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Hera Nadeem
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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16
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From protein biomarkers to proteomics in dementia with Lewy Bodies. Ageing Res Rev 2023; 83:101771. [PMID: 36328346 DOI: 10.1016/j.arr.2022.101771] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/15/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative dementia. Despite considerable research progress, there remain gaps in our understanding of the pathophysiology and there is no disease-modifying treatment. Proteomics is a powerful tool to elucidate complex biological pathways across heterogenous conditions. This review summarizes the widely used proteomic methods and presents evidence for protein dysregulation in the brain and peripheral tissues in DLB. Proteomics of post-mortem brain tissue shows that DLB shares common features with other dementias, such as synaptic dysfunction, but retains a unique protein signature. Promising diagnostic biomarkers are being identified in cerebrospinal fluid (CSF), blood, and peripheral tissues, such as serum Heart-type fatty acid binding protein. Research is needed to track these changes from the prodromal stage to established dementia, with standardized workflows to ensure replicability. Identifying novel protein targets in causative biological pathways could lead to the development of new targeted therapeutics or the stratification of participants for clinical trials.
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17
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Cai Y, Zhou Z, Zhu ZJ. Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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Mohd Kamal K, Mahamad Maifiah MH, Zhu Y, Abdul Rahim N, Hashim YZHY, Abdullah Sani MS. Isotopic Tracer for Absolute Quantification of Metabolites of the Pentose Phosphate Pathway in Bacteria. Metabolites 2022; 12:1085. [PMID: 36355168 PMCID: PMC9697766 DOI: 10.3390/metabo12111085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 10/18/2023] Open
Abstract
The pentose phosphate pathway (PPP) plays a key role in many metabolic functions, including the generation of NADPH, biosynthesis of nucleotides, and carbon homeostasis. In particular, the intermediates of PPP have been found to be significantly perturbed in bacterial metabolomic studies. Nonetheless, detailed analysis to gain mechanistic information of PPP metabolism remains limited as most studies are unable to report on the absolute levels of the metabolites. Absolute quantification of metabolites is a prerequisite to study the details of fluxes and its regulations. Isotope tracer or labeling studies are conducted in vivo and in vitro and have significantly improved the analysis and understanding of PPP. Due to the laborious procedure and limitations in the in vivo method, an in vitro approach known as Group Specific Internal Standard Technology (GSIST) has been successfully developed to measure the absolute levels of central carbon metabolism, including PPP. The technique adopts derivatization of an experimental sample and a corresponding internal standard with isotope-coded reagents to provide better precision for accurate identification and absolute quantification. In this review, we highlight bacterial studies that employed isotopic tracers as the tagging agents used for the absolute quantification analysis of PPP metabolites.
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Affiliation(s)
- Khairunnisa Mohd Kamal
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), Jalan Gombak 53100, Selangor, Malaysia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), Jalan Gombak 53100, Selangor, Malaysia
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Nusaibah Abdul Rahim
- Faculty of Pharmacy, University of Malaya, Kuala Lumpur 50603, Selangor, Malaysia
| | - Yumi Zuhanis Has-Yun Hashim
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), Jalan Gombak 53100, Selangor, Malaysia
| | - Muhamad Shirwan Abdullah Sani
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), Jalan Gombak 53100, Selangor, Malaysia
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19
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Rise K, Tessem MB, Drabløs F, Rye MB. FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer. PLoS One 2022; 17:e0275621. [PMID: 36282866 PMCID: PMC9595552 DOI: 10.1371/journal.pone.0275621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial activity in cancer cells has been central to cancer research since Otto Warburg first published his thesis on the topic in 1956. Although Warburg proposed that oxidative phosphorylation in the tricarboxylic acid (TCA) cycle was perturbed in cancer, later research has shown that oxidative phosphorylation is activated in most cancers, including prostate cancer (PCa). However, more detailed knowledge on mitochondrial metabolism and metabolic pathways in cancers is still lacking. In this study we expand our previously developed method for analyzing functional homologous proteins (FunHoP), which can provide a more detailed view of metabolic pathways. FunHoP uses results from differential expression analysis of RNA-Seq data to improve pathway analysis. By adding information on subcellular localization based on experimental data and computational predictions we can use FunHoP to differentiate between mitochondrial and non-mitochondrial processes in cancerous and normal prostate cell lines. Our results show that mitochondrial pathways are upregulated in PCa and that splitting metabolic pathways into mitochondrial and non-mitochondrial counterparts using FunHoP adds to the interpretation of the metabolic properties of PCa cells.
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Affiliation(s)
- Kjersti Rise
- Department of Clinical and Molecular Medicine, NTNU–Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail: (MBR); (KR)
| | - May-Britt Tessem
- Department of Circulation and Medical Imaging, NTNU–Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU–Norwegian University of Science and Technology, Trondheim, Norway
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, NTNU–Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore—Bioinformatics Core Facility, NTNU–Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail: (MBR); (KR)
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20
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Carper DL, Appidi MR, Mudbhari S, Shrestha HK, Hettich RL, Abraham PE. The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont. Microorganisms 2022; 10:microorganisms10102013. [PMID: 36296289 PMCID: PMC9609723 DOI: 10.3390/microorganisms10102013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Sameer Mudbhari
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence:
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21
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Chabi K, Sleno L. Estradiol, Estrone and Ethinyl Estradiol Metabolism Studied by High Resolution LC-MS/MS Using Stable Isotope Labeling and Trapping of Reactive Metabolites. Metabolites 2022; 12:metabo12100931. [PMID: 36295833 PMCID: PMC9611524 DOI: 10.3390/metabo12100931] [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] [Received: 08/27/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Biotransformation reactions that xenobiotics undergo during their metabolism are crucial for their proper excretion from the body, but can also be a source of toxicity, especially in the case of reactive metabolite formation. Unstable, reactive metabolites are capable of covalent binding to proteins, and have often been linked to liver damage and other undesired side effects. A common technique to assess the formation of reactive metabolites employs trapping them in vitro with glutathione and characterizing the resulting adducts by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Some endogenous compounds, however, can interfere with xenobiotic metabolites of interest, making the analysis more difficult. This study demonstrates the usefulness of isotope-labeled compounds to detect and elucidate the structures of both stable metabolites and trapped adducts of three estrogen analogs using an untargeted LC-MS/MS workflow. The metabolism of estradiol, estrone and ethinyl estradiol was investigated. Unlabeled and deuterated versions of these three compounds were incubated with human or rat liver microsomes in the presence of two different trapping agents, namely glutathione and N-acetylcysteine. The detection of closely eluting deuterated peaks allowed us to confirm the formation of several known metabolites, as well as many previously uncharacterized ones. The structure of each adduct was elucidated by the detailed analysis of high-resolution MS/MS spectra for elucidating fragmentation pathways with accurate mass measurements. The use of isotopic labeling was crucial in helping confirm many metabolites and adduct structures, as well as removing endogenous interferences.
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22
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Snyder KA, Robinson SA, Schmidt S, Hultine KR. Stable isotope approaches and opportunities for improving plant conservation. CONSERVATION PHYSIOLOGY 2022; 10:coac056. [PMID: 35966756 PMCID: PMC9367551 DOI: 10.1093/conphys/coac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 04/15/2021] [Accepted: 08/01/2022] [Indexed: 06/01/2023]
Abstract
Successful conservation of threatened species and ecosystems in a rapidly changing world requires scientifically sound decision-making tools that are readily accessible to conservation practitioners. Physiological applications that examine how plants and animals interact with their environment are now widely used when planning, implementing and monitoring conservation. Among these tools, stable-isotope physiology is a potentially powerful, yet under-utilized cornerstone of current and future conservation efforts of threatened and endangered plants. We review the underlying concepts and theory of stable-isotope physiology and describe how stable-isotope applications can support plant conservation. We focus on stable isotopes of carbon, hydrogen, oxygen and nitrogen to address plant ecophysiological responses to changing environmental conditions across temporal scales from hours to centuries. We review examples from a broad range of plant taxa, life forms and habitats and provide specific examples where stable-isotope analysis can directly improve conservation, in part by helping identify resilient, locally adapted genotypes or populations. Our review aims to provide a guide for practitioners to easily access and evaluate the information that can be derived from stable-isotope signatures, their limitations and how stable isotopes can improve conservation efforts.
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Affiliation(s)
- Keirith A Snyder
- Corresponding author: USDA Agricultural Research Service, Great Basin Rangelands Research Unit, Reno,
920 Valley Road, NV 89512, USA.
| | - Sharon A Robinson
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Securing Antarctica’s Environmental Future, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Sciences, The University of Queensland, Building 62, Brisbane Queensland 4075, Australia
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 Galvin Parkway, Phoenix, AZ 85008, USA
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23
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Li H, Lai Z, Peng M, Ning L, Dong Q, Hou Y, An J. One-Pot Sequential Hydrogen Isotope Exchange/Reductive Deuteration for the Preparation of α,β-Deuterated Alcohols using Deuterium Oxide. Org Lett 2022; 24:5319-5323. [PMID: 35856804 DOI: 10.1021/acs.orglett.2c01940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An efficient one-pot sequential hydrogen isotope exchange (HIE)/reductive deuteration approach was developed for the preparation of α,β-deuterated alcohols using ketones as the precursors. The HIE step can also be used for the synthesis of α-deuterated ketones. This method has been applied in the synthesis of four deuterated drug and MS internal standards.
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Affiliation(s)
- Hengzhao Li
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.,Department of Chemistry and Innovation Center of Pesticide Research, China Agricultural University, Beijing 100193, China
| | - Zemin Lai
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Mengqi Peng
- Department of Chemistry and Innovation Center of Pesticide Research, China Agricultural University, Beijing 100193, China
| | - Lei Ning
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Qixin Dong
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yuxia Hou
- Department of Chemistry and Innovation Center of Pesticide Research, China Agricultural University, Beijing 100193, China
| | - Jie An
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
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24
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Alcolombri U, Pioli R, Stocker R, Berry D. Single-cell stable isotope probing in microbial ecology. ISME COMMUNICATIONS 2022; 2:55. [PMID: 37938753 PMCID: PMC9723680 DOI: 10.1038/s43705-022-00142-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/10/2022] [Accepted: 06/09/2022] [Indexed: 05/30/2023]
Abstract
Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.
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Affiliation(s)
- Uria Alcolombri
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roberto Pioli
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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A rapid and robust method for amino acid quantification using a simple N-hydroxysuccinimide ester derivatization and liquid chromatography-ion mobility-mass spectrometry. Anal Bioanal Chem 2022; 414:5549-5559. [PMID: 35338375 DOI: 10.1007/s00216-022-03993-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/01/2022]
Abstract
The vast majority of mass spectrometry (MS)-based metabolomics studies employ reversed-phase liquid chromatography (RPLC) to separate analytes prior to MS detection. Highly polar metabolites, such as amino acids (AAs), are poorly retained by RPLC, making quantitation of these key species challenging across the broad concentration ranges typically observed in biological specimens, such as cell extracts. To improve the detection and quantitation of AAs in microglial cell extracts, the implementation of a 4-dimethylaminobenzoylamido acetic acid N-hydroxysuccinimide ester (DBAA-NHS) derivatization agent was explored for its ability to improve both analyte retention and detection limits in RPLC-MS. In addition to the introduction of the DBAA-NHS labeling reagent, a uniformly (U) 13C-labeled yeast extract was also introduced during the sample preparation workflow as an internal standard (IS) to eliminate artifacts and to enable targeted quantitation of AAs, as well as untargeted amine submetabolome profiling. To improve method sensitivity and selectivity, multiplexed drift-tube ion mobility (IM) was integrated into the LC-MS workflow, facilitating the separation of isomeric metabolites, and improving the structural identification of unknown metabolites. Implementation of the U-13C-labeled yeast extract during the multiplexed LC-IM-MS analysis enabled the quantitation of 19 of the 20 common AAs, supporting a linear dynamic range spanning up to three orders of magnitude in concentration for microglial cell extracts, in addition to reducing the required cell count for reliable quantitation from 10 to 5 million cells per sample.
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De Craemer S, Driesen K, Ghesquière B. TraVis Pies: A Guide for Stable Isotope Metabolomics Interpretation Using an Intuitive Visualization. Metabolites 2022; 12:metabo12070593. [PMID: 35888717 PMCID: PMC9321460 DOI: 10.3390/metabo12070593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Tracer metabolomics is a powerful technology for the biomedical community to study and understand disease-inflicted metabolic mechanisms. However, the interpretation of tracer metabolomics results is highly technical, as the metabolites’ abundances, tracer incorporation and positions on the metabolic map all must be jointly interpreted. The field is currently lacking a structured approach to help less experienced researchers start the interpretation of tracer metabolomics datasets. We propose an approach using an intuitive visualization concept aided by a novel open-source tool, and provide guidelines on how researchers can apply the approach and the visualization tool to their own datasets. Using a showcase experiment, we demonstrate that the visualization approach leads to an intuitive interpretation that can ease researchers into understanding their tracer metabolomics data.
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Affiliation(s)
- Sam De Craemer
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium;
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Correspondence: (S.D.C.); (B.G.)
| | - Karen Driesen
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium;
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium;
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Correspondence: (S.D.C.); (B.G.)
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Butin N, Bergès C, Portais JC, Bellvert F. An optimization method for untargeted MS-based isotopic tracing investigations of metabolism. Metabolomics 2022; 18:41. [PMID: 35713733 PMCID: PMC9205802 DOI: 10.1007/s11306-022-01897-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Stable isotope tracer studies are increasingly applied to explore metabolism from the detailed analysis of tracer incorporation into metabolites. Untargeted LC/MS approaches have recently emerged and provide potent methods for expanding the dimension and complexity of the metabolic networks that can be investigated. A number of software tools have been developed to process the highly complex MS data collected in such studies; however, a method to optimize the extraction of valuable isotopic data is lacking. OBJECTIVES To develop and validate a method to optimize automated data processing for untargeted MS-based isotopic tracing investigations of metabolism. METHODS The method is based on the application of a suitable reference material to rationally perform parameter optimization throughout the complete data processing workflow. It was applied in the context of 13C-labelling experiments and with two different software, namely geoRge and X13CMS. It was illustrated with the study of a E. coli mutant impaired for central metabolism. RESULTS The optimization methodology provided significant gain in the number and quality of extracted isotopic data, independently of the software considered. Pascal triangle samples are well suited for such purpose since they allow both the identification of analytical issues and optimization of data processing at the same time. CONCLUSION The proposed method maximizes the biological value of untargeted MS-based isotopic tracing investigations by revealing the full metabolic information that is encoded in the labelling patterns of metabolites.
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Affiliation(s)
- Noémie Butin
- RESTORE, CNRS ERL5311, EFS, ENVT, Inserm U1031, UPS, Université de Toulouse, Toulouse, France
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Cécilia Bergès
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Jean-Charles Portais
- RESTORE, CNRS ERL5311, EFS, ENVT, Inserm U1031, UPS, Université de Toulouse, Toulouse, France
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Floriant Bellvert
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France.
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.
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Rey-Stolle F, Dudzik D, Gonzalez-Riano C, Fernández-García M, Alonso-Herranz V, Rojo D, Barbas C, García A. Low and high resolution gas chromatography-mass spectrometry for untargeted metabolomics: A tutorial. Anal Chim Acta 2022; 1210:339043. [PMID: 35595356 DOI: 10.1016/j.aca.2021.339043] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/28/2022]
Abstract
GC-MS for untargeted metabolomics is a well-established technique. Small molecules and molecules made volatile by derivatization can be measured and those compounds are key players in main biological pathways. This tutorial provides ready-to-use protocols for GC-MS-based metabolomics, using either the well-known low-resolution approach (GC-Q-MS) with nominal mass or the more recent high-resolution approach (GC-QTOF-MS) with accurate mass, discussing their corresponding strengths and limitations. Analytical procedures are covered for different types of biofluids (plasma/serum, bronchoalveolar lavage, urine, amniotic fluid) tissue samples (brain/hippocampus, optic nerve, lung, kidney, liver, pancreas) and samples obtained from cell cultures (adipocytes, macrophages, Leishmania promastigotes, mitochondria, culture media). Together with the sample preparation and data acquisition, data processing strategies are described specially focused on Agilent equipments, including deconvolution software and database annotation using spectral libraries. Manual curation strategies and quality control are also deemed. Finally, considerations to obtain a semiquantitative value for the metabolites are also described. As a case study, an illustrative example from one of our experiments at CEMBIO Research Centre, is described and findings discussed.
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Affiliation(s)
- Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain
| | - Danuta Dudzik
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain; Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy, Medical University of Gdańsk, Poland
| | - Carolina Gonzalez-Riano
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain
| | - Miguel Fernández-García
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain
| | - Vanesa Alonso-Herranz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain
| | - Antonia García
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, CEU Universities. Campus Monteprincipe, Boadilla Del Monte, 28668, Madrid, Spain.
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Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [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] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
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Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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An isotopic labeling approach linking natural products with biosynthetic gene clusters. Nat Chem Biol 2022; 18:295-304. [PMID: 34969972 PMCID: PMC8891042 DOI: 10.1038/s41589-021-00949-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/29/2021] [Indexed: 12/31/2022]
Abstract
Major advances in genome sequencing and large-scale biosynthetic gene cluster (BGC) analysis have prompted an age of natural product discovery driven by genome mining. Still, connecting molecules to their cognate BGCs is a substantial bottleneck for this approach. We have developed a mass-spectrometry-based parallel stable isotope labeling platform, termed IsoAnalyst, which assists in associating metabolite stable isotope labeling patterns with BGC structure prediction to connect natural products to their corresponding BGCs. Here we show that IsoAnalyst can quickly associate both known metabolites and unknown analytes with BGCs to elucidate the complex chemical phenotypes of these biosynthetic systems. We validate this approach for a range of compound classes, using both the type strain Saccharopolyspora erythraea and an environmentally isolated Micromonospora sp. We further demonstrate the utility of this tool with the discovery of lobosamide D, a new and structurally unique member of the family of lobosamide macrolactams.
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Metabolomics as an emerging tool to study plant–microbe interactions. Emerg Top Life Sci 2022; 6:175-183. [PMID: 35191478 PMCID: PMC9023012 DOI: 10.1042/etls20210262] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 01/14/2023]
Abstract
In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant–microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant–microbe interaction studies discussing current challenges and future prospects.
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Seidl B, Schuhmacher R, Bueschl C. CPExtract, a Software Tool for the Automated Tracer-Based Pathway Specific Screening of Secondary Metabolites in LC-HRMS Data. Anal Chem 2022; 94:3543-3552. [PMID: 35166525 PMCID: PMC8892430 DOI: 10.1021/acs.analchem.1c04530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The use of stable
isotopically labeled tracers is a long-proven
way of specifically detecting and tracking derived metabolites through
a metabolic network of interest. While the recently developed stable
isotope-assisted methods and associated, supporting data analysis
tools have greatly improved untargeted metabolomics approaches, no
software tool is currently available that allows us to automatically
and flexibly search liquid chromatography coupled with high-resolution
mass spectrometry (LC-HRMS) chromatograms for user-definable isotopolog
patterns expected for the metabolism of labeled tracer substances.
Here, we present Custom Pattern Extract (CPExtract), a versatile software
tool that allows for the first time the high-throughput search for
user-defined isotopolog patterns in LC-HRMS data. The patterns can
be specified via a set of rules including the presence or absence
of certain isotopologs, their relative intensity ratios as well as
chromatographic coelution. Each isotopolog pattern satisfying the
respective rules is verified on an MS scan level and also in the chromatographic
domain. The CPExtract algorithm allows the use of both labeled tracer
compounds in nonlabeled biological samples as well as a reversed tracer
approach, employing nonlabeled tracer compounds along with globally
labeled biological samples. In a proof-of-concept study, we searched
for metabolites specifically arising from the malonate pathway of
the filamentous fungi Fusarium graminearum and Trichoderma reesei. 1,2,3-13C3-malonic acid diethyl ester and native malonic
acid monomethyl ester were used as tracers. We were able to reliably
detect expected fatty acids and known polyketides. In addition, up
to 46 and 270 further, unknown metabolites presumably including novel
polyketides were detected in the F. graminearum and T. reesei culture samples, respectively,
all of which exhibited the user-predicted isotopolog patterns originating
from the malonate tracer incorporation. The software can be used for
every conceivable tracer approach. Furthermore, the rule sets can
be easily adapted or extended if necessary. CPExtract is available
free of charge for noncommercial use at https://metabolomics-ifa.boku.ac.at/CPExtract.
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Affiliation(s)
- Bernhard Seidl
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Christoph Bueschl
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
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Dodds JN, Wang L, Patti GJ, Baker ES. Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses. Anal Chem 2022; 94:2527-2535. [PMID: 35089687 PMCID: PMC8934380 DOI: 10.1021/acs.analchem.1c04430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments, ensuring these prioritized features originate from endogenous metabolism remains challenging. Isotopologue workflows, such as isotopic ratio outlier analysis (IROA), mass isotopomer ratio analysis of U-13C labeled extracts (MIRACLE), and credentialing incorporate isotopic labels directly into metabolic precursors, guaranteeing that all features of interest are unequivocal byproducts of cellular metabolism. Furthermore, comprehensive separation and annotation of small molecules continue to challenge the metabolomics field, particularly for isomeric systems. In this paper, we evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) as an additional separation mechanism into standard LC-MS/MS isotopologue workflows. Since isotopically labeled molecules codrift in the IMS dimension with their 12C versions, LC-IMS-CID-MS provides four dimensions (LC, IMS, MS, and MS/MS) to directly investigate the metabolic activity of prioritized untargeted features. Here, we demonstrate this additional selectivity by showcasing how a preliminary data set of 30 endogeneous metabolites are putatively annotated from isotopically labeled Escherichia coli cultures when analyzed by LC-IMS-CID-MS. Metabolite annotations were based on several molecular descriptors, including accurate mass measurement, carbon number, annotated fragmentation spectra, and collision cross section (CCS), collectively illustrating the importance of incorporating IMS into isotopologue workflows. Overall, our results highlight the enhanced separation space and increased annotation confidence afforded by IMS for metabolic characterization and provide a unique perspective for future developments in isotopically labeled MS experiments.
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Affiliation(s)
| | | | - Gary J. Patti
- Departments of Chemistry and Medicine, Siteman Cancer Center, Center for Metabolomics and Isotope Tracing, Washington University, St. Louis, Missouri 63130, United States
| | - Erin S. Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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Hubert CB, de Carvalho LPS. Metabolomic approaches for enzyme function and pathway discovery in bacteria. Methods Enzymol 2022; 665:29-47. [DOI: 10.1016/bs.mie.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Flasch M, Bueschl C, Del Favero G, Adam G, Schuhmacher R, Marko D, Warth B. Elucidation of xenoestrogen metabolism by non-targeted, stable isotope-assisted mass spectrometry in breast cancer cells. ENVIRONMENT INTERNATIONAL 2022; 158:106940. [PMID: 34673318 DOI: 10.1016/j.envint.2021.106940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Environmental exposure to xenoestrogens, i.e., chemicals that imitate the hormone 17β-estradiol, has the potential to influence hormone homeostasis and action. Detailed knowledge of xenobiotic biotransformation processes in cell models is key when transferring knowledge learned from in vitro models to in vivo relevance. This study elucidated the metabolism of two naturally-occurring phyto- and mycoestrogens; namely genistein and zearalenone, in an estrogen receptor positive breast cancer cell line (MCF-7) with the aid of stable isotope-assisted metabolomics and the bioinformatic tool MetExtract II. Metabolism was studied in a time course experiment after 2 h, 6 h and 24 h incubation. Twelve and six biotransformation products of zearalenone and genistein were detected, respectively, clearly demonstrating the abundant xenobiotic biotransformation capability of the cells. Zearalenone underwent extensive phase-I metabolism resulting in α-zearalenol (α-ZEL), a molecule known to possess a significantly higher estrogenicity, and several phase-II metabolites (sulfo- and glycoconjugates) of the native compound and the major phase I metabolite α-ZEL. Moreover, potential adducts of zearalenone with a vitamin and several hydroxylated metabolites were annotated. Genistein metabolism resulted in sulfation, combined sulfation and hydroxylation, acetylation, glucuronidation and unexpectedly adduct formation with pentose- and hexose sugars. Kinetics of metabolite formation and subsequent excretion into the extracellular medium revealed a time-dependent increase in most biotransformation products. The untargeted elucidation of biotransformation products formed during cell culture experiments enables an improved and more meaningful interpretation of toxicological assays and has the potential to identify unexpected or unknown metabolites.
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Affiliation(s)
- Mira Flasch
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria
| | - Christoph Bueschl
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Str. 20, 3430 Tulln, Austria; University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Giorgia Del Favero
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria
| | - Gerhard Adam
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, Konrad-Lorenz-Str. 24, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Doris Marko
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Str. 38, 1090 Vienna, Austria.
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Eylem CC, Reçber T, Waris M, Kır S, Nemutlu E. State-of-the-art GC-MS approaches for probing central carbon metabolism. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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37
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Liu M, Jiang J, Zheng J, Huan T, Gao B, Fei X, Wang Y, Fang M. RTP: One Effective Platform to Probe Reactive Compound Transformation Products and Its Applications for a Reactive Plasticizer BADGE. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16034-16043. [PMID: 34788994 DOI: 10.1021/acs.est.1c05262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Reactive compounds, such as covalent toxicants/drugs, have their ubiquitous occurrences and are known to react with protein or DNA in human beings, but their reactions with endogenous metabolites are rarely understood. Currently, a viable platform is demanded for discovering their reaction products since their efficacy/toxicity may be altered after the reaction. We aim to develop a platform for identifying unknown abiotic or biotransformation products for these reactive compounds. Based on stable isotope-labeling (SIL) metabolomics, we have developed a novel and robust analytical platform, reactive compound transformation profiler (RTP), which can automatically analyze preannotated high-resolution mass spectrometry (LC-HRMS) data sets and uncover probable transformation products. Generally, RTP consists of four complementary steps: (1) selecting peak pairs of light and heavy-labeled products, (2) defining the "core structure mass" for possible reaction search, (3) constructing an endogenous metabolite reaction database, and (4) developing algorithms to propose the potential transformation products by searching against the database with a single-/multiple-site reaction. Its performance was validated using the reactive plasticizer bisphenol A diglycidyl ether (BADGE) in several sample matrices. This platform enabled the identification of novel transformation products while also demonstrating its capacity to filter out the false-positive signals and provide product annotation. The RTP is freely accessible at https://github.com/FangLabNTU/Reactive-Compound-Transformation-Profiler-RTP-.
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Affiliation(s)
- Min Liu
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, 637141 Singapore
| | - Jie Jiang
- School of Computer Science and Engineering, Nanyang Technological University, 639798 Singapore
| | - Jie Zheng
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Avenue, 636921 Singapore
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xunchang Fei
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Avenue, 636921 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, 637141 Singapore
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Shen D, Lu Z, Zhong J, Zhang S, Ye Q, Wang W, Gan J. Combination of high specific activity carbon-14 labeling and high resolution mass spectrometry to study pesticide metabolism in crops: Metabolism of cycloxaprid in rice. ENVIRONMENT INTERNATIONAL 2021; 157:106879. [PMID: 34543936 DOI: 10.1016/j.envint.2021.106879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/02/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
The study of pesticide metabolism in crops is critical for assessing the mode of action and environmental risks of pesticides. However, the study of pesticide metabolism in crops is usually complicated and it is often a daunting challenge to accurately screen the metabolites of novel pesticides in complex matrices. This study demonstrated a combined use of high-specific activity carbon-14 labeling and high-resolution mass spectrometry (HSA-14C-HRMS) for metabolism profiling of a novel neonicotinoid cycloxaprid in rice. By generating the characteristic radioactive peaks on the liquid chromatogram, the use of 14C can eliminate the severe interference of complex matrices and quickly probe target compounds; by producing ion pairs with unique abundance ratios on HRMS, high-specific activity labeling can effectively exclude false matrix positives and promote the elucidation of metabolite structure. The structures of 15 metabolites were identified, three of which were further confirmed by authentic standards. Based on these metabolites, a metabolic profile of cycloxaprid was established, which includes denitrification, demethylation, imidazolidine hydroxylation and ring cleavage olefin formation, oxidation and carboxylation reactions. The strategy of combining high-specific activity 14C labeling and HRMS offers unique advantages and provides a powerful solution for profiling unknown metabolites of novel pesticides in complex matrices, especially when traditional non-labeling methods are not feasible.
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Affiliation(s)
- Dahang Shen
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Zhijiang Lu
- Department of Environmental Science and Geology, Wayne State University, Detroit, MI 48202, USA
| | - Jiayin Zhong
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Sufen Zhang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Qingfu Ye
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Wei Wang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
| | - Jay Gan
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
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Yu D, Zheng F, Wang L, Li C, Lu X, Lin X, Zhou L, Xu G. Novel Stable Isotope-Resolved Metabolomics Method for a Small Number of Cells Using Chip-Based Nanoelectrospray Mass Spectrometry. Anal Chem 2021; 93:13765-13773. [PMID: 34606241 DOI: 10.1021/acs.analchem.1c01507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable isotope-resolved metabolomics (SIRM) can provide metabolic conversion information of specific targets; it is a powerful tool for cell metabolism studies. The common analytical platform for SIRM is chromatography-mass spectrometry, which requires a large number of cells and is not suitable for precious rare cell analysis. To study a small number of cells, we established a novel SIRM method using chip-based nanoelectrospray mass spectrometry (MS). 13C-glutamine was taken as an example; the unlabeled and 13C-labeled cells were cultured and extracted in a 96-well plate and then directly injected into MS and analyzed in full scan mode and parallel reaction monitoring (PRM) mode targeting 44 glutamine-derived metabolites and their isotopologues. To define focused metabolite-related MS2 fragments produced in the PRM, a new strategy was proposed including MS2 exact m/z matching, MS2 false positive filtering, and MS2 fragment grouping to remove the interfering MS2 ions. In total, 292 and 349 pairs of paired MS2 ions were obtained in positive and negative ionization modes, respectively. By searching spectra databases, 31 targeted metabolites with their isotopologues were identified and their characteristic product ions were confirmed for MS2 quantification. The relative quantification was achieved by MS2 quantification, which showed better sensitivity and accuracy than common MS1-based quantification. Finally, this method was applied to isocitrate dehydrogenase I-mutated glioma cells for revealing the effects of triptolide on glioma cell metabolism using U-13C-glutamine as a labeling substrate.
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Affiliation(s)
- Di Yu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichao Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Li
- School of Computer Science & Technology, Dalian University of Technology, Dalian 116024, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaohui Lin
- School of Computer Science & Technology, Dalian University of Technology, Dalian 116024, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Lin W, Conway LP, Vujasinovic M, Löhr J, Globisch D. Chemoselective and Highly Sensitive Quantification of Gut Microbiome and Human Metabolites. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Weifeng Lin
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
| | - Louis P. Conway
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases Karolinska University Hospital Stockholm Sweden
| | - J.‐Matthias Löhr
- Department for Digestive Diseases Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science Intervention and Technology (CLINTEC) Karolinska Institute Stockholm Sweden
| | - Daniel Globisch
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
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Kumar K, Bruheim P. A comparative study at bioprocess and metabolite levels of superhost strain Streptomyces coelicolor M1152 and its derivative M1581 heterologously expressing chloramphenicol biosynthetic gene cluster. Biotechnol Bioeng 2021; 119:145-161. [PMID: 34636422 DOI: 10.1002/bit.27958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/20/2021] [Accepted: 10/03/2021] [Indexed: 11/09/2022]
Abstract
Microbial superhost strains should provide an ideal platform for the efficient homologous or heterologous phenotypic expression of biosynthetic gene clusters (BGCs) of new and novel bioactive molecules. Our aim in the current study was to perform a comparative study at the bioprocess and metabolite levels of the previously designed superhost strain Streptomyces coelicolor M1152 and its derivative strain S. coelicolor M1581 heterologously expressing chloramphenicol BGC. Parent strain M1152 was characterized by a higher specific growth rate, specific CO2 evolution rate, and a higher specific l-glutamate consumption rate as compared with M1581. Intracellular primary central metabolites (nucleoside/sugar phosphates, amino acids, organic acids, and CoAs) were quantified using four targeted LC-MS/MS-based methods. The metabolite pathways in the nonantibiotic producing S. coelicolor host strain were flooded with carbon from both carbon sources, whereas in antibiotic-producing strain, the carbon of l-glutamate seems to be draining out through excreting synthesized antibiotic. The 13 C-isotope-labeling experiments revealed the bidirectionality in the glycolytic pathway and reversibility in the non-oxidative part of PPP even with continuous uptake of d-glucose. The change in the primary metabolites due to the insertion of BGC disclosed a clear linkage between the primary and secondary metabolites.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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42
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Lin W, Conway LP, Vujasinovic M, Löhr JM, Globisch D. Chemoselective and highly sensitive quantification of gut microbiome and human metabolites. Angew Chem Int Ed Engl 2021; 60:23232-23240. [PMID: 34339587 PMCID: PMC8597006 DOI: 10.1002/anie.202107101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Indexed: 11/18/2022]
Abstract
The microbiome has a fundamental impact on the human host's physiology through the production of highly reactive compounds that can lead to disease development. One class of such compounds are carbonyl‐containing metabolites, which are involved in diverse biochemical processes. Mass spectrometry is the method of choice for analysis of metabolites but carbonyls are analytically challenging. Herein, we have developed a new chemical biology tool using chemoselective modification to overcome analytical limitations. Two isotopic probes allow for the simultaneous and semi‐quantitative analysis at the femtomole level as well as qualitative analysis at attomole quantities that allows for detection of more than 200 metabolites in human fecal, urine and plasma samples. This comprehensive mass spectrometric analysis enhances the scope of metabolomics‐driven biomarker discovery. We anticipate that our chemical biology tool will be of general use in metabolomics analysis to obtain a better understanding of microbial interactions with the human host and disease development.
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Affiliation(s)
- Weifeng Lin
- Uppsala University: Uppsala Universitet, Dept. Chemistry - BMC, Uppsala, SWEDEN
| | - Louis P Conway
- Uppsala University: Uppsala Universitet, Dept. Chem. - BMC, 75421, Uppsala, SWEDEN
| | - Miroslav Vujasinovic
- Karolinska University Hospital: Karolinska Universitetssjukhuset, Dept. for Digestive Diseases, Stockholm, SWEDEN
| | - J-Matthias Löhr
- Karolinska Institute: Karolinska Institutet, Dept. Clinical Science, Intervention and Technology, Stockholm, SWEDEN
| | - Daniel Globisch
- Uppsala University, Department of Medicinal Chemistry, Husaragatan 3, Biomedical Center, Box 574, 75123, Uppsala, SWEDEN
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Straub M, Sigman DM, Auderset A, Ollivier J, Petit B, Hinnenberg B, Rubach F, Oleynik S, Vozenin MC, Martínez-García A. Distinct nitrogen isotopic compositions of healthy and cancerous tissue in mice brain and head&neck micro-biopsies. BMC Cancer 2021; 21:805. [PMID: 34256713 PMCID: PMC8276491 DOI: 10.1186/s12885-021-08489-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cancerous cells can recycle metabolic ammonium for their growth. As this ammonium has a low nitrogen isotope ratio (15N/14N), its recycling may cause cancer tissue to have lower 15N/14N than surrounding healthy tissue. We investigated whether, within a given tissue type in individual mice, tumoral and healthy tissues could be distinguished based on their 15N/14N. METHODS Micro-biopsies of murine tumors and adjacent tissues were analyzed for 15N/14N using novel high-sensitivity methods. Isotopic analysis was pursued in Nude and C57BL/6 mice models with mature orthotopic brain and head&neck tumors generated by implantation of H454 and MEERL95 murine cells, respectively. RESULTS In the 7 mice analyzed, the brain tumors had distinctly lower 15N/14N than healthy neural tissue. In the 5 mice with head&neck tumors, the difference was smaller and more variable. This was at least partly due to infiltration of healthy head&neck tissue by tumor cells. However, it may also indicate that the 15N/14N difference between tumoral and healthy tissue depends on the nitrogen metabolism of the healthy organ in question. CONCLUSIONS The findings, coupled with the high sensitivity of the 15N/14N measurement method used here, suggest a new approach for micro-biopsy-based diagnosis of malignancy as well as an avenue for investigation of cancer metabolism.
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Affiliation(s)
- M Straub
- Institute of Radiation Physics, Lausanne University Hospital and University of Lausanne, 1007 Lausanne, Switzerland.
- Max Planck Institute for Chemistry, 55128, Mainz, Germany.
| | - D M Sigman
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - A Auderset
- Max Planck Institute for Chemistry, 55128, Mainz, Germany
| | - J Ollivier
- Radiation Oncology Laboratory/DO/Radio-Oncology/CHUV, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - B Petit
- Radiation Oncology Laboratory/DO/Radio-Oncology/CHUV, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - B Hinnenberg
- Max Planck Institute for Chemistry, 55128, Mainz, Germany
| | - F Rubach
- Max Planck Institute for Chemistry, 55128, Mainz, Germany
| | - S Oleynik
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - M-C Vozenin
- Radiation Oncology Laboratory/DO/Radio-Oncology/CHUV, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
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Furukawa K, Toyomizu M, Kikusato M. Possible role of corticosterone in proteolysis, glycolytic, and amino acid metabolism in primary cultured avian myotubes incubated at high-temperature conditions. Domest Anim Endocrinol 2021; 76:106608. [PMID: 33611161 DOI: 10.1016/j.domaniend.2021.106608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 12/05/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Excess glucocorticoid secretion induces oxidative damage and muscle proteolysis and modulates glucose and lipid metabolism. It is known that the high-temperature (HT) treatment enhances corticosterone (CORT) secretion, muscle proteolysis, and mitochondrial reactive oxygen species (mtROS) generation in chickens. The present study investigated the co-effects of CORT on proteolysis and mtROS production, together with glucose, fatty acid, and amino acid metabolism in HT-treated cells. Myoblast cells were isolated from the major pectoralis muscle of five 0- or 1-day-old neonatal chicks and were precultured at 37°C/CO2 conditions for 48 h to reach subconfluent (80%-90%) conditions. Cells were then reseeded onto a 6- or 24-well microplate for the subsequent measurement, followed by the culture under a control temperature (37°C, control) or HT (41°C) conditions for 1 or 6 h. The HT-treated cells were cocultured with physiologically relevant concentrations of CORT (20 ng/mL in dimethyl sulfoxide). The HT treatment decreased cellular protein content (P < 0.05) and increased atrogin-1 mRNA levels and mtROS generation levels compared to the control group (P < 0.05), whereas HT/CORT co-treatment did not induce changes in either parameter. The mRNA level of glucose transporter-1 was decreased in HT-treated cells compared to that in normal cells (P < 0.05), and the decrease was increased in the CORT co-treatment (P < 0.05). While HT treatment did not alter pyruvate dehydrogenase kinase-4 mRNA level, the level was increased in the CORT co-treatment compared to the control and HT-treated cells (P < 0.05). Neither HT nor HT/CORT treatments altered the mRNA levels of fatty acid oxidation-related factors, carnitine palmitoyl transferase-1, and cluster of differentiation 36. The study conducted a metabolic analysis using gas chromatography-mass spectrometry. The results showed that HT/CORT-treated cells had decreased intracellular citrate and α-ketoglutarate levels (P < 0.05) and increased extracellular alanine and amino acid that have gluconeogenic properties, as well as increased aspartate, isoleucine, serine, methionine, and threonine levels (P < 0.05) compared to HT-treated cells. These results suggest that CORT may not affect proteolysis and mtROS production but can suppress pyruvate oxidation and promote alanine production in HT-treated chickens.
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Affiliation(s)
- Kyohei Furukawa
- Animal Nutrition, Life Sciences, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8572, Japan
| | - Masaaki Toyomizu
- Animal Nutrition, Life Sciences, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8572, Japan
| | - Motoi Kikusato
- Animal Nutrition, Life Sciences, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8572, Japan.
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45
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Rao Y, Gammon ST, Sutton MN, Zacharias NM, Bhattacharya P, Piwnica-Worms D. Excess exogenous pyruvate inhibits lactate dehydrogenase activity in live cells in an MCT1-dependent manner. J Biol Chem 2021; 297:100775. [PMID: 34022218 PMCID: PMC8233206 DOI: 10.1016/j.jbc.2021.100775] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Cellular pyruvate is an essential metabolite at the crossroads of glycolysis and oxidative phosphorylation, capable of supporting fermentative glycolysis by reduction to lactate mediated by lactate dehydrogenase (LDH) among other functions. Several inherited diseases of mitochondrial metabolism impact extracellular (plasma) pyruvate concentrations, and [1-13C]pyruvate infusion is used in isotope-labeled metabolic tracing studies, including hyperpolarized magnetic resonance spectroscopic imaging. However, how these extracellular pyruvate sources impact intracellular metabolism is not clear. Herein, we examined the effects of excess exogenous pyruvate on intracellular LDH activity, extracellular acidification rates (ECARs) as a measure of lactate production, and hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion rates across a panel of tumor and normal cells. Combined LDH activity and LDHB/LDHA expression analysis intimated various heterotetrameric isoforms comprising LDHA and LDHB in tumor cells, not only canonical LDHA. Millimolar concentrations of exogenous pyruvate induced substrate inhibition of LDH activity in both enzymatic assays ex vivo and in live cells, abrogated glycolytic ECAR, and inhibited hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion rates in cellulo. Of importance, the extent of exogenous pyruvate-induced inhibition of LDH and glycolytic ECAR in live cells was highly dependent on pyruvate influx, functionally mediated by monocarboxylate transporter-1 localized to the plasma membrane. These data provided evidence that highly concentrated bolus injections of pyruvate in vivo may transiently inhibit LDH activity in a tissue type- and monocarboxylate transporter-1-dependent manner. Maintaining plasma pyruvate at submillimolar concentrations could potentially minimize transient metabolic perturbations, improve pyruvate therapy, and enhance quantification of metabolic studies, including hyperpolarized [1-13C]pyruvate magnetic resonance spectroscopic imaging and stable isotope tracer experiments.
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Affiliation(s)
- Yi Rao
- Department of Cancer System Imaging, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Seth T Gammon
- Department of Cancer System Imaging, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Margie N Sutton
- Department of Cancer System Imaging, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Niki M Zacharias
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Pratip Bhattacharya
- Department of Cancer System Imaging, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - David Piwnica-Worms
- Department of Cancer System Imaging, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.
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Jin H, Moseley HNB. Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases. Metabolites 2021; 11:metabo11070431. [PMID: 34209357 PMCID: PMC8307411 DOI: 10.3390/metabo11070431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Metabolic models have been proven to be useful tools in system biology and have been successfully applied to various research fields in a wide range of organisms. A relatively complete metabolic network is a prerequisite for deriving reliable metabolic models. The first step in constructing metabolic network is to harmonize compounds and reactions across different metabolic databases. However, effectively integrating data from various sources still remains a big challenge. Incomplete and inconsistent atomistic details in compound representations across databases is a very important limiting factor. Here, we optimized a subgraph isomorphism detection algorithm to validate generic compound pairs. Moreover, we defined a set of harmonization relationship types between compounds to deal with inconsistent chemical details while successfully capturing atom-level characteristics, enabling a more complete enabling compound harmonization across metabolic databases. In total, 15,704 compound pairs across KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc databases were detected. Furthermore, utilizing the classification of compound pairs and EC (Enzyme Commission) numbers of reactions, we established hierarchical relationships between metabolic reactions, enabling the harmonization of 3856 reaction pairs. In addition, we created and used atom-specific identifiers to evaluate the consistency of atom mappings within and between harmonized reactions, detecting some consistency issues between the reaction and compound descriptions in these metabolic databases.
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Affiliation(s)
- Huan Jin
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA;
| | - Hunter N. B. Moseley
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Superfund Research Center, University of Kentucky, Lexington, KY 40506, USA
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY 40536, USA
- Correspondence: ; Tel.: +1-859-218-2964
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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48
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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Kim SH, Kim H, Jeong H, Yoon TY. Encoding Multiple Virtual Signals in DNA Barcodes with Single-Molecule FRET. NANO LETTERS 2021; 21:1694-1701. [PMID: 33586985 DOI: 10.1021/acs.nanolett.0c04502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
DNA barcoding provides a way to label a myriad of different biological molecules using the extreme programmability in DNA sequence synthesis. Fluorescence imaging is presumably the most easy-to-access method for DNA barcoding, yet large spectral overlaps between fluorescence dyes severely limit the numbers of barcodes that can be detected simultaneously. We here demonstrate the use of single-molecule fluorescence resonance energy transfer (FRET) to encode virtual signals in DNA barcodes using conventional two-color fluorescence microscopy. By optimizing imaging and biochemistry conditions for weak DNA hybridization events, we markedly enhanced accuracy in our determination of the single-molecule FRET efficiency exhibited by each binding event between DNA barcode sequences. This allowed us to unambiguously differentiate six DNA barcodes encoding different FRET values without involving any probe sequence exchanges. Our method can be directly incorporated with previous DNA barcode techniques, and may thus be widely adopted to expand the signal space of DNA barcoding.
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Affiliation(s)
- Sung Hyun Kim
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Hyunwoo Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Hawoong Jeong
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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50
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Xu R, Wang Y, Du J. Tracing Nitrogen Metabolism in Mouse Tissues with Gas Chromatography-Mass Spectrometry. Bio Protoc 2021; 11:e3925. [PMID: 33732812 DOI: 10.21769/bioprotoc.3925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 11/02/2022] Open
Abstract
Nitrogen-containing metabolites including ammonia, amino acids, and nucleotides, are essential for cell metabolism, growth, and neural transmission. Nitrogen metabolism is tightly coordinated with carbon metabolism in the breakdown and biosynthesis of amino acids and nucleotides. Both nuclear magnetic resonance spectroscopy and mass spectrometry including gas chromatography-mass spectrometry (GC MS) and liquid chromatography (LC MS) have been used to measure nitrogen metabolism. Here we describe a protocol to trace nitrogen metabolism in multiple mouse tissues using 15N-ammonia coupled with GC MS. This protocol includes detailed procedures in tracer injection, tissue preparation, metabolite extraction, GC MS analysis and natural abundance corrections. This protocol will provide a useful tool to study tissue-specific nitrogen in metabolically active tissues such as the retina, brain, liver, and tumor.
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Affiliation(s)
- Rong Xu
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, USA.,Department of Biochemistry, West Virginia University, Morgantown, USA
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, USA.,Department of Biochemistry, West Virginia University, Morgantown, USA
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, USA.,Department of Biochemistry, West Virginia University, Morgantown, USA
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