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Repkin EA, Gafarova ER, Varfolomeeva MA, Kurjachii DS, Polev DE, Shavarda AL, Maslakov GP, Mullakhmetov RI, Zubova EV, Bariev TB, Granovitch AI, Maltseva AL. Littorina snails and Microphallus trematodes: Diverse consequences of the trematode-induced metabolic shifts. Parasitol Res 2024; 123:229. [PMID: 38819740 DOI: 10.1007/s00436-024-08244-8] [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: 09/03/2023] [Accepted: 05/18/2024] [Indexed: 06/01/2024]
Abstract
The intricate relationships between parasites and hosts encompass a wide range of levels, from molecular interactions to population dynamics. Parasites influence not only the physiological processes in the host organism, but also the entire ecosystem, affecting mortality of individuals, the number of offspring through parasitic castration, and matter and energy cycles. Understanding the molecular mechanisms that govern host-parasite relationships and their impact on host physiology and environment remains challenging. In this study, we analyzed how infection with Microphallus trematodes affects the metabolome of two Littorina snail species inhabiting different intertidal zone shore levels. We applied non-targeted GC-MS-based metabolomics to analyze biochemical shifts induced by trematode infection in a host organism. We have identified changes in energy, amino acid, sugar, and lipid metabolism. In particular, we observed intensified amino acid catabolism and nitrogenous catabolites (glutamine, urea) production. These changes primarily correlated with infection and interspecies differences of the hosts rather than shore level. The changes detected in the host metabolism indicate that other aspects of life may have been affected, both within the host organism and at a supra-organismal level. Therefore, we explored changes in microbiota composition, deviations in the host molluscs behavior, and acetylcholinesterase activity (ACE, an enzyme involved in neuromuscular transmission) in relation to infection. Infected snails displayed changes in their microbiome composition. Decreased ACE activity in snails was associated with reduced mobility, but whether it is associated with trematode infection remains unclear. The authors suggest a connection between the identified biochemical changes and the deformation of the shell of molluscs, changes in their behavior, and the associated microbiome. The role of parasitic systems formed by microphallid trematodes and Littorina snails in the nitrogen cycle at the ecosystem level is also assumed.
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Affiliation(s)
- Egor A Repkin
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia.
- Research Park Centre for Molecular and Cell Technologies, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia.
| | - Elizaveta R Gafarova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Dmitrii S Kurjachii
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Dmitrii E Polev
- Department of Epidemiology, St. Petersburg Pasteur Institute, 197101 Mira Street 14, St. Petersburg, Russia
| | - Alexei L Shavarda
- Research Park Centre for Molecular and Cell Technologies, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
- Department of Analytical Phytochemistry, Komarov Botanical Institute, 197376 Professora Popova Street 2, St. Petersburg, Russia
| | - Georgiy P Maslakov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Roman I Mullakhmetov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Ekaterina V Zubova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Timur B Bariev
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
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2
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Kotronoulas A, de Lomana ALG, Einarsdóttir HK, Kjartansson H, Stone R, Rolfsson Ó. Fish Skin Grafts Affect Adenosine and Methionine Metabolism during Burn Wound Healing. Antioxidants (Basel) 2023; 12:2076. [PMID: 38136196 PMCID: PMC10741162 DOI: 10.3390/antiox12122076] [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: 11/02/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Burn wound healing is a complex process orchestrated through successive biochemical events that span from weeks to months depending on the depth of the wound. Here, we report an untargeted metabolomics discovery approach to capture metabolic changes during the healing of deep partial-thickness (DPT) and full-thickness (FT) burn wounds in a porcine burn wound model. The metabolic changes during healing could be described with six and seven distinct metabolic trajectories for DPT and FT wounds, respectively. Arginine and histidine metabolism were the most affected metabolic pathways during healing, irrespective of burn depth. Metabolic proxies for oxidative stress were different in the wound types, reaching maximum levels at day 14 in DPT burns but at day 7 in FT burns. We examined how acellular fish skin graft (AFSG) influences the wound metabolome compared to other standard-or-care burn wound treatments. We identified changes in metabolites within the methionine salvage pathway, specifically in DPT burn wounds that is novel to the understanding of the wound healing process. Furthermore, we found that AFSGs boost glutamate and adenosine in wounds that is of relevance given the importance of purinergic signaling in regulating oxidative stress and wound healing. Collectively, these results serve to define biomarkers of burn wound healing. These results conclusively contribute to the understanding of the multifactorial mechanism of the action of AFSG that has traditionally been attributed to its structural properties and omega-3 fatty acid content.
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Affiliation(s)
- Aristotelis Kotronoulas
- Center for Systems Biology, Medical Department, University of Iceland, Sturlugata 8, 102 Reykjavik, Iceland
| | | | | | | | - Randolph Stone
- US Army Institute of Surgical Research, JBSA Fort Sam Houston, TX 78234, USA
| | - Óttar Rolfsson
- Center for Systems Biology, Medical Department, University of Iceland, Sturlugata 8, 102 Reykjavik, Iceland
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3
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Bullert A, Li X, Chunyun Z, Lee K, Pulliam CF, Cagle BS, Doorn JA, Klingelhutz AJ, Robertson LW, Lehmler HJ. Disposition and metabolomic effects of 2,2',5,5'-tetrachlorobiphenyl in female rats following intraperitoneal exposure. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 102:104245. [PMID: 37572994 PMCID: PMC10562985 DOI: 10.1016/j.etap.2023.104245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
The disposition and toxicity of lower chlorinated PCBs (LC-PCBs) with less than five chlorine substituents have received little attention. This study characterizes the distribution and metabolomic effects of PCB 52, an LC-PCB found in indoor and outdoor air, three weeks after intraperitoneal exposure of female Sprague Dawley rats to 0, 1, 10, or 100 mg/kg BW. PCB 52 exposure did not affect overall body weight. Gas chromatography-tandem mass spectrometry (GC-MS/MS) analysis identified PCB 52 in all tissues investigated. Hydroxylated, sulfated, and methylated PCB metabolites, identified using GC-MS/MS and nontarget liquid chromatography-high resolution mass spectrometry (Nt-LCMS), were primarily found in the serum and liver of rats exposed to 100 mg/kg BW. Metabolomic analysis revealed minor effects on L-cysteine, glycine, cytosine, sphingosine, thymine, linoleic acid, orotic acid, L-histidine, and erythrose serum levels. Thus, the metabolism of PCB 52 and its effects on the metabolome must be considered in toxicity studies.
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Affiliation(s)
- Amanda Bullert
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
| | - Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Zhang Chunyun
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Kendra Lee
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Casey F Pulliam
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
| | - Brianna S Cagle
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - Jonathan A Doorn
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA; Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - Aloysius J Klingelhutz
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Larry W Robertson
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA.
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4
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Bullert A, Li X, Zhang C, Lee K, Pulliam CF, Cagle BS, Doorn JA, Klingelhutz AJ, Robertson LW, Lehmler HJ. Disposition and Metabolomic Effects of 2,2',5,5'-Tetrachlorobiphenyl in Female Rats Following Intraperitoneal Exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.19.544952. [PMID: 37609242 PMCID: PMC10441371 DOI: 10.1101/2023.06.19.544952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The disposition and toxicity of lower chlorinated PCBs (LC-PCBs) with less than five chlorine substituents have received little attention. This study characterizes the distribution and metabolomic effects of PCB 52, an LC-PCB found in indoor and outdoor air, three weeks after intraperitoneal exposure of female Sprague Dawley rats to 0, 1, 10, or 100 mg/kg BW. PCB 52 exposure did not affect overall body weight. Gas chromatography-tandem mass spectrometry (GC-MS/MS) analysis identified PCB 52 in all tissues investigated. Hydroxylated, sulfated, and methylated PCB metabolites, identified using GC-MS/MS and nontarget liquid chromatography-high resolution mass spectrometry (Nt-LCMS), were primarily found in the serum and liver of rats exposed to 100 mg/kg BW. Metabolomic analysis revealed minor effects on L-cysteine, glycine, cytosine, sphingosine, thymine, linoleic acid, orotic acid, L-histidine, and erythrose serum levels. Thus, the metabolism of PCB 52 and its effects on the metabolome must be considered in toxicity studies. Highlights PCB 52 was present in adipose, brain, liver, and serum 3 weeks after PCB exposureLiver and serum contained hydroxylated, sulfated, and methylated PCB 52 metabolitesMetabolomics analysis revealed minor changes in endogenous serum metabolitesLevels of dopamine and its metabolites in the brain were not affected by PCB 52.
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Affiliation(s)
- Amanda Bullert
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
| | - Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Chunyun Zhang
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Kendra Lee
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Casey F. Pulliam
- Interdisciplinary Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
| | - Brianna S. Cagle
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - Jonathan A. Doorn
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - Aloysius J. Klingelhutz
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Larry W. Robertson
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
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5
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Brunnsåker D, Reder GK, Soni NK, Savolainen OI, Gower AH, Tiukova IA, King RD. High-throughput metabolomics for the design and validation of a diauxic shift model. NPJ Syst Biol Appl 2023; 9:11. [PMID: 37029131 PMCID: PMC10082077 DOI: 10.1038/s41540-023-00274-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
Saccharomyces cerevisiae is a very well studied organism, yet ∼20% of its proteins remain poorly characterized. Moreover, recent studies seem to indicate that the pace of functional discovery is slow. Previous work has implied that the most probable path forward is via not only automation but fully autonomous systems in which active learning is applied to guide high-throughput experimentation. Development of tools and methods for these types of systems is of paramount importance. In this study we use constrained dynamical flux balance analysis (dFBA) to select ten regulatory deletant strains that are likely to have previously unexplored connections to the diauxic shift. We then analyzed these deletant strains using untargeted metabolomics, generating profiles which were then subsequently investigated to better understand the consequences of the gene deletions in the metabolic reconfiguration of the diauxic shift. We show that metabolic profiles can be utilised to not only gaining insight into cellular transformations such as the diauxic shift, but also on regulatory roles and biological consequences of regulatory gene deletion. We also conclude that untargeted metabolomics is a useful tool for guidance in high-throughput model improvement, and is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of genes. Moreover, it is well-suited for automated approaches due to relative simplicity of processing and the potential to make massively high-throughput.
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Affiliation(s)
- Daniel Brunnsåker
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
| | - Gabriel K Reder
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Nikul K Soni
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Otto I Savolainen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Alexander H Gower
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Ievgeniia A Tiukova
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ross D King
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Alan Turing Institute, London, UK
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6
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Fu J, Zhu F, Xu CJ, Li Y. Metabolomics meets systems immunology. EMBO Rep 2023; 24:e55747. [PMID: 36916532 PMCID: PMC10074123 DOI: 10.15252/embr.202255747] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/24/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.
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Affiliation(s)
- Jianbo Fu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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Steward KF, Refai M, Dyer WE, Copié V, Lachowiec J, Bothner B. Acute stress reduces population-level metabolic and proteomic variation. BMC Bioinformatics 2023; 24:87. [PMID: 36882728 PMCID: PMC9993721 DOI: 10.1186/s12859-023-05185-4] [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: 04/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Variation in omics data due to intrinsic biological stochasticity is often viewed as a challenging and undesirable feature of complex systems analyses. In fact, numerous statistical methods are utilized to minimize the variation among biological replicates. RESULTS We demonstrate that the common statistics relative standard deviation (RSD) and coefficient of variation (CV), which are often used for quality control or part of a larger pipeline in omics analyses, can also be used as a metric of a physiological stress response. Using an approach we term Replicate Variation Analysis (RVA), we demonstrate that acute physiological stress leads to feature-wide canalization of CV profiles of metabolomes and proteomes across biological replicates. Canalization is the repression of variation between replicates, which increases phenotypic similarity. Multiple in-house mass spectrometry omics datasets in addition to publicly available data were analyzed to assess changes in CV profiles in plants, animals, and microorganisms. In addition, proteomics data sets were evaluated utilizing RVA to identify functionality of reduced CV proteins. CONCLUSIONS RVA provides a foundation for understanding omics level shifts that occur in response to cellular stress. This approach to data analysis helps characterize stress response and recovery, and could be deployed to detect populations under stress, monitor health status, and conduct environmental monitoring.
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Affiliation(s)
- Katherine F Steward
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Mohammed Refai
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - William E Dyer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.,Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.,Thermal Biology Institute, Montana State University, Bozeman, USA
| | - Jennifer Lachowiec
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA. .,Thermal Biology Institute, Montana State University, Bozeman, USA.
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Fabrile MP, Ghidini S, Conter M, Varrà MO, Ianieri A, Zanardi E. Filling gaps in animal welfare assessment through metabolomics. Front Vet Sci 2023; 10:1129741. [PMID: 36925610 PMCID: PMC10011658 DOI: 10.3389/fvets.2023.1129741] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Sustainability has become a central issue in Italian livestock systems driving food business operators to adopt high standards of production concerning animal husbandry conditions. Meat sector is largely involved in this ecological transition with the introduction of new label claims concerning the defense of animal welfare (AW). These new guarantees referred to AW provision require new tools for the purpose of authenticity and traceability to assure meat supply chain integrity. Over the years, European Union (EU) Regulations, national, and international initiatives proposed provisions and guidelines for assuring AW introducing requirements to be complied with and providing tools based on scoring systems for a proper animal status assessment. However, the comprehensive and objective assessment of the AW status remains challenging. In this regard, phenotypic insights at molecular level may be investigated by metabolomics, one of the most recent high-throughput omics techniques. Recent advances in analytical and bioinformatic technologies have led to the identification of relevant biomarkers involved in complex clinical phenotypes of diverse biological systems suggesting that metabolomics is a key tool for biomarker discovery. In the present review, the Five Domains model has been employed as a vademecum describing AW. Starting from the individual Domains-nutrition (I), environment (II), health (III), behavior (IV), and mental state (V)-applications and advances of metabolomics related to AW setting aimed at investigating phenotypic outcomes on molecular scale and elucidating the biological routes most perturbed from external solicitations, are reviewed. Strengths and weaknesses of the current state-of-art are highlighted, and new frontiers to be explored for AW assessment throughout the metabolomics approach are argued. Moreover, a detailed description of metabolomics workflow is provided to understand dos and don'ts at experimental level to pursue effective results. Combining the demand for new assessment tools and meat market trends, a new cross-strategy is proposed as the promising combo for the future of AW assessment.
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Affiliation(s)
| | - Sergio Ghidini
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Mauro Conter
- Department of Veterinary Science, University of Parma, Parma, Italy
| | | | - Adriana Ianieri
- Department of Food and Drug, University of Parma, Parma, Italy
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Du X, Dastmalchi F, Ye H, Garrett TJ, Diller MA, Liu M, Hogan WR, Brochhausen M, Lemas DJ. Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software. Metabolomics 2023; 19:11. [PMID: 36745241 DOI: 10.1007/s11306-023-01974-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a popular approach for metabolomics data acquisition and requires many data processing software tools. The FAIR Principles - Findability, Accessibility, Interoperability, and Reusability - were proposed to promote open science and reusable data management, and to maximize the benefit obtained from contemporary and formal scholarly digital publishing. More recently, the FAIR principles were extended to include Research Software (FAIR4RS). AIM OF REVIEW This study facilitates open science in metabolomics by providing an implementation solution for adopting FAIR4RS in the LC-HRMS metabolomics data processing software. We believe our evaluation guidelines and results can help improve the FAIRness of research software. KEY SCIENTIFIC CONCEPTS OF REVIEW We evaluated 124 LC-HRMS metabolomics data processing software obtained from a systematic review and selected 61 software for detailed evaluation using FAIR4RS-related criteria, which were extracted from the literature along with internal discussions. We assigned each criterion one or more FAIR4RS categories through discussion. The minimum, median, and maximum percentages of criteria fulfillment of software were 21.6%, 47.7%, and 71.8%. Statistical analysis revealed no significant improvement in FAIRness over time. We identified four criteria covering multiple FAIR4RS categories but had a low %fulfillment: (1) No software had semantic annotation of key information; (2) only 6.3% of evaluated software were registered to Zenodo and received DOIs; (3) only 14.5% of selected software had official software containerization or virtual machine; (4) only 16.7% of evaluated software had a fully documented functions in code. According to the results, we discussed improvement strategies and future directions.
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Affiliation(s)
- Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Farhad Dastmalchi
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Hao Ye
- Health Science Center Libraries, University of Florida, Florida, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Florida, USA
| | - Matthew A Diller
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mei Liu
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - William R Hogan
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA.
- Department of Obstetrics and Gynecology, University of Florida College of Medicine, Florida, Gainesville, United States.
- Center for Perinatal Outcomes Research, University of Florida College of Medicine, Gainesville, United States.
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10
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Saponara E, Penno C, Orsini V, Wang ZY, Fischer A, Aebi A, Matadamas-Guzman ML, Brun V, Fischer B, Brousseau M, O'Donnell P, Turner J, Graff Meyer A, Bollepalli L, d'Ario G, Roma G, Carbone W, Annunziato S, Obrecht M, Beckmann N, Saravanan C, Osmont A, Tropberger P, Richards SM, Genoud C, Ley S, Ksiazek I, Nigsch F, Terracciano LM, Schadt HS, Bouwmeester T, Tchorz JS, Ruffner H. Loss of Hepatic Leucine-Rich Repeat-Containing G-Protein Coupled Receptors 4 and 5 Promotes Nonalcoholic Fatty Liver Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:161-181. [PMID: 36410420 DOI: 10.1016/j.ajpath.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 11/19/2022]
Abstract
The roof plate-specific spondin-leucine-rich repeat-containing G-protein coupled receptor 4/5 (LGR4/5)-zinc and ring finger 3 (ZNRF3)/ring finger protein 43 (RNF43) module is a master regulator of hepatic Wnt/β-catenin signaling and metabolic zonation. However, its impact on nonalcoholic fatty liver disease (NAFLD) remains unclear. The current study investigated whether hepatic epithelial cell-specific loss of the Wnt/β-catenin modulator Lgr4/5 promoted NAFLD. The 3- and 6-month-old mice with hepatic epithelial cell-specific deletion of both receptors Lgr4/5 (Lgr4/5dLKO) were compared with control mice fed with normal diet (ND) or high-fat diet (HFD). Six-month-old HFD-fed Lgr4/5dLKO mice developed hepatic steatosis and fibrosis but the control mice did not. Serum cholesterol-high-density lipoprotein and total cholesterol levels in 3- and 6-month-old HFD-fed Lgr4/5dLKO mice were decreased compared with those in control mice. An ex vivo primary hepatocyte culture assay and a comprehensive bile acid (BA) characterization in liver, plasma, bile, and feces demonstrated that ND-fed Lgr4/5dLKO mice had impaired BA secretion, predisposing them to develop cholestatic characteristics. Lipidome and RNA-sequencing analyses demonstrated severe alterations in several lipid species and pathways controlling lipid metabolism in the livers of Lgr4/5dLKO mice. In conclusion, loss of hepatic Wnt/β-catenin activity by Lgr4/5 deletion led to loss of BA secretion, cholestatic features, altered lipid homeostasis, and deregulation of lipoprotein pathways. Both BA and intrinsic lipid alterations contributed to the onset of NAFLD.
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Affiliation(s)
- Enrica Saponara
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carlos Penno
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Zhong-Yi Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Audrey Fischer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Aebi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Meztli L Matadamas-Guzman
- Instituto Nacional de Medicina Genómica-Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Virginie Brun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Benoit Fischer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Margaret Brousseau
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Peter O'Donnell
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Jonathan Turner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Graff Meyer
- Friedrich Miescher Institute for BioMedical Research, Facility for Advanced Imaging and Microscopy, Basel, Switzerland
| | - Laura Bollepalli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Giovanni d'Ario
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Stefano Annunziato
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Michael Obrecht
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nicolau Beckmann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Chandra Saravanan
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Arnaud Osmont
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp Tropberger
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Shola M Richards
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Svenja Ley
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Luigi M Terracciano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Istituto di Ricovero e Cura a Carattere Scientifico, Humanitas Research Hospital, Anatomia Patologica, Rozzano, Milan, Italy
| | - Heiko S Schadt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Heinz Ruffner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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11
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Rong Z, Liu Z, Song J, Cao L, Yu Y, Qiu M, Hou Y. MCluster-VAEs: An end-to-end variational deep learning-based clustering method for subtype discovery using multi-omics data. Comput Biol Med 2022; 150:106085. [PMID: 36162197 DOI: 10.1016/j.compbiomed.2022.106085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/30/2022] [Accepted: 09/03/2022] [Indexed: 11/03/2022]
Abstract
The discovery of cancer subtypes based on unsupervised clustering helps in providing a precise diagnosis, guide treatment, and improve patients' prognoses. Instead of single-omics data, multi-omics data can improve the clustering performance because it obtains a comprehensive landscape for understanding biological systems and mechanisms. However, heterogeneous data from multiple sources raises high complexity and different kinds of noise, which are detrimental to the extraction of clustering information. We propose an end-to-end deep learning based method, called Multi-omics Clustering Variational Autoencoders (MCluster-VAEs), that can extract cluster-friendly representations on multi-omics data. First, a unified network architecture with an attention mechanism was developed for accurately modeling multi-omics data. Then, using a novel objective function built from the Variational Bayes technique, the model was trained to effectively obtain the posterior estimation of the clustering assignments. Compared with 12 other state-of-the-art multi-omics clustering methods, MCluster-VAEs achieved an outstanding performance on benchmark datasets from the TCGA database. On the Pan Cancer dataset, MCluster-VAEs achieved an adjusted Rand index of approximately 0.78 for cancer category recognition, an increase of more than 18% compared with other methods. Furthermore, a survival analysis and clinical parameter enrichment tests conducted on 10 cancer datasets demonstrated that MCluster-VAEs provides comparable and even better results than many common integrative approaches. These results demonstrate that MCluster-VAEs are a powerful new tool for dissecting complex multi-omics relationships and providing new insights for cancer subtype discovery.
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Affiliation(s)
- Zhiwei Rong
- Department of Biostatistics Beijing, Peking University School of Public Health, No. 38 Xueyuan Road, Haidian District, Beijing, 100000, China
| | - Zhilin Liu
- Department of Biostatistics Beijing, Peking University School of Public Health, No. 38 Xueyuan Road, Haidian District, Beijing, 100000, China
| | - Jiali Song
- Department of Biostatistics Beijing, Peking University School of Public Health, No. 38 Xueyuan Road, Haidian District, Beijing, 100000, China
| | - Lei Cao
- Department of Epidemiology and Biostatistics Harbin, Harbin Medical University School of Public Health, Harbin, 150000, Heilongjiang, China
| | - Yipe Yu
- Department of Biostatistics Beijing, Peking University School of Public Health, No. 38 Xueyuan Road, Haidian District, Beijing, 100000, China
| | - Mantang Qiu
- Department of Thoracic Surgery Beijing, Peking University People's Hospital, Beijing, 100000, China.
| | - Yan Hou
- Department of Biostatistics Beijing, Peking University School of Public Health, No. 38 Xueyuan Road, Haidian District, Beijing, 100000, China; Peking University Clinical Research Center, No. 38 Xueyuan Road, Haidian District, Beijing, 100000, China.
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12
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Diagnosis and prognosis of COVID-19 employing analysis of patients' plasma and serum via LC-MS and machine learning. Comput Biol Med 2022; 146:105659. [PMID: 35751188 PMCID: PMC9123826 DOI: 10.1016/j.compbiomed.2022.105659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To implement and evaluate machine learning (ML) algorithms for the prediction of COVID-19 diagnosis, severity, and fatality and to assess biomarkers potentially associated with these outcomes. MATERIAL AND METHODS Serum (n = 96) and plasma (n = 96) samples from patients with COVID-19 (acute, severe and fatal illness) from two independent hospitals in China were analyzed by LC-MS. Samples from healthy volunteers and from patients with pneumonia caused by other viruses (i.e. negative RT-PCR for COVID-19) were used as controls. Seven different ML-based models were built: PLS-DA, ANNDA, XGBoostDA, SIMCA, SVM, LREG and KNN. RESULTS The PLS-DA model presented the best performance for both datasets, with accuracy rates to predict the diagnosis, severity and fatality of COVID-19 of 93%, 94% and 97%, respectively. Low levels of the metabolites ribothymidine, 4-hydroxyphenylacetoylcarnitine and uridine were associated with COVID-19 positivity, whereas high levels of N-acetyl-glucosamine-1-phosphate, cysteinylglycine, methyl isobutyrate, l-ornithine and 5,6-dihydro-5-methyluracil were significantly related to greater severity and fatality from COVID-19. CONCLUSION The PLS-DA model can help to predict SARS-CoV-2 diagnosis, severity and fatality in daily practice. Some biomarkers typically increased in COVID-19 patients' serum or plasma (i.e. ribothymidine, N-acetyl-glucosamine-1-phosphate, l-ornithine, 5,6-dihydro-5-methyluracil) should be further evaluated as prognostic indicators of the disease.
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13
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Yu H, Huan T. MAFFIN: Metabolomics Sample Normalization Using Maximal Density Fold Change with High-Quality Metabolic Features and Corrected Signal Intensities. Bioinformatics 2022; 38:3429-3437. [PMID: 35639662 DOI: 10.1093/bioinformatics/btac355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/18/2022] [Accepted: 05/19/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Post-acquisition sample normalization is a critical step in comparative metabolomics to remove the variation introduced by sample amount or concentration difference. Previously reported approaches are either specific to one sample type or built on strong assumptions on data structure, which are limited to certain levels. This encouraged us to develop MAFFIN, an accurate and robust post-acquisition sample normalization workflow that works universally for metabolomics data collected on mass spectrometry (MS) platforms. RESULTS MAFFIN calculates normalization factors using maximal density fold change (MDFC) computed by a kernel density-based approach. Using both simulated data and 20 metabolomics data sets, we showcased that MDFC outperforms four commonly used normalization methods in terms of reducing the intragroup variation among samples. Two essential steps, overlooked in conventional methods, were also examined and incorporated into MAFFIN. (1) MAFFIN uses multiple orthogonal criteria to select high-quality features for normalization factor calculation, which minimizes the bias caused by abiotic features or metabolites with poor quantitative performance. (2) MAFFIN corrects the MS signal intensities of high-quality features using serial quality control (QC) samples, which guarantees the accuracy of fold change calculations. MAFFIN was applied to a human saliva metabolomics study and led to better data separation in principal component analysis (PCA) and more confirmed significantly altered metabolites. AVAILABILITY AND IMPLEMENTATION The MAFFIN algorithm was implemented in an R package named MAFFIN. Package installation, user instruction, and demo data are available at https://github.com/HuanLab/MAFFIN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Huaxu Yu
- Department of Chemistry, Faculty of Science, The University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Tao Huan
- Department of Chemistry, Faculty of Science, The University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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14
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Metabolic Response in Endothelial Cells to Catecholamine Stimulation Associated with Increased Vascular Permeability. Int J Mol Sci 2022; 23:ijms23063162. [PMID: 35328583 PMCID: PMC8950318 DOI: 10.3390/ijms23063162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 02/07/2023] Open
Abstract
Disruption to endothelial cell homeostasis results in an extensive variety of human pathologies that are particularly relevant to major trauma. Circulating catecholamines, such as adrenaline and noradrenaline, activate endothelial adrenergic receptors triggering a potent response in endothelial function. The regulation of the endothelial cell metabolism is distinct and profoundly important to endothelium homeostasis. However, a precise catalogue of the metabolic alterations caused by sustained high catecholamine levels that results in endothelial dysfunction is still underexplored. Here, we uncover a set of up to 46 metabolites that exhibit a dose–response relationship to adrenaline-noradrenaline equimolar treatment. The identified metabolites align with the glutathione-ascorbate cycle and the nitric oxide biosynthesis pathway. Certain key metabolites, such as arginine and reduced glutathione, displayed a differential response to treatment in early (4 h) compared to late (24 h) stages of sustained stimulation, indicative of homeostatic metabolic feedback loops. Furthermore, we quantified an increase in the glucose consumption and aerobic respiration in endothelial cells upon catecholamine stimulation. Our results indicate that oxidative stress and nitric oxide metabolic pathways are downstream consequences of endothelial cell stimulation with sustained high levels of catecholamines. A precise understanding of the metabolic response in endothelial cells to pathological levels of catecholamines will facilitate the identification of more efficient clinical interventions in trauma patients.
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15
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Dubois E, Galindo AN, Dayon L, Cominetti O. Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples. Biosystems 2022; 215-216:104661. [PMID: 35247480 DOI: 10.1016/j.biosystems.2022.104661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinical research study, from human biological sample collection and storage, sample preparation, spectral data acquisition, to peptide and protein quantification. In order to remove such diverse and unwanted variability, normalization of the protein data is performed. There have been already several published reviews comparing normalization methods in the -omics field, but reports focusing on proteomic data generated with mass spectrometry (MS) are much fewer. Additionally, most of these reports have only dealt with small datasets. RESULTS As a case study, here we focused on the normalization of a large MS-based proteomic dataset obtained from an overweight and obese pan-European cohort, where different normalization methods were evaluated, namely: center standardize, quantile protein, quantile sample, global standardization, ComBat, median centering, mean centering, single standard and removal of unwanted variation (RUV); some of these are generic normalization methods while others have been specifically created to deal with genomic or metabolomic data. We checked how relationships between proteins and clinical variables (e.g., gender, levels of triglycerides or cholesterol) were improved after normalizing the data with the different methods. CONCLUSIONS Some normalization methods were better adapted for this particular large-scale shotgun proteomic dataset of human plasma samples labeled with isobaric tags and analyzed with liquid chromatography-tandem MS. In particular, quantile sample normalization, RUV, mean and median centering showed very good performance, while quantile protein normalization provided worse results than those obtained with unnormalized data.
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Affiliation(s)
- Etienne Dubois
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland; Chemistry and Chemical Engineering Section, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, EPFL Innovation Park, 1015, Lausanne, Switzerland.
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16
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Simonsen D, Cady N, Zhang C, Shrode RL, McCormick ML, Spitz DR, Chimenti MS, Wang K, Mangalam A, Lehmler HJ. The Effects of Benoxacor on the Liver and Gut Microbiome of C57BL/6 Mice. Toxicol Sci 2022; 186:102-117. [PMID: 34850242 PMCID: PMC9019840 DOI: 10.1093/toxsci/kfab142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The toxicity of many "inert" ingredients of pesticide formulations, such as safeners, is poorly characterized, despite evidence that humans may be exposed to these chemicals. Analysis of ToxCast data for dichloroacetamide safeners with the ToxPi tool identified benoxacor as the safener with the highest potential for toxicity, especially liver toxicity. Benoxacor was subsequently administered to mice via oral gavage for 3 days at concentrations of 0, 0.5, 5, and 50 mg/kg bodyweight (b.w.). Bodyweight-adjusted liver and testes weights were significantly increased in the 50 mg/kg b.w. group. There were no overt pathologies in either the liver or the intestine. 16S rRNA analysis of the cecal microbiome revealed no effects of benoxacor on α- or β-diversity; however, changes were observed in the abundance of certain bacteria. RNAseq analysis identified 163 hepatic genes affected by benoxacor exposure. Benoxacor exposure expressed a gene regulation profile similar to dichloroacetic acid and the fungicide sedaxane. Metabolomic analysis identified 9 serum and 15 liver metabolites that were affected by benoxacor exposure, changes that were not significant after correcting for multiple comparisons. The activity of antioxidant enzymes was not altered by benoxacor exposure. In vitro metabolism studies with liver microsomes and cytosol from male mice demonstrated that benoxacor is enantioselectively metabolized by cytochrome P450 enzymes, carboxylesterases, and glutathione S-transferases. These findings suggest that the minor toxic effects of benoxacor may be due to its rapid metabolism to toxic metabolites, such as dichloroacetic acid. This result challenges the assumption that inert ingredients of pesticide formulations are safe.
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Affiliation(s)
- Derek Simonsen
- Department of Occupational and Environmental Health, The University of Iowa, Iowa City, Iowa 52242, USA
- Interdisciplinary Graduate Program in Human Toxicology, The University of Iowa, Iowa City, Iowa 52242, USA
- IIHR Hydroscience and Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Nicole Cady
- Department of Pathology, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Chunyun Zhang
- Department of Occupational and Environmental Health, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Rachel L Shrode
- Department of Informatics, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Michael L McCormick
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Douglas R Spitz
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Kai Wang
- Department of Biostatistics, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Ashutosh Mangalam
- Department of Pathology, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, The University of Iowa, Iowa City, Iowa 52242, USA
- Interdisciplinary Graduate Program in Human Toxicology, The University of Iowa, Iowa City, Iowa 52242, USA
- IIHR Hydroscience and Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
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17
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Boolani A, Gallivan KM, Ondrak KS, Christopher CJ, Castro HF, Campagna SR, Taylor CM, Luo M, Dowd SE, Smith ML, Byerley LO. Trait Energy and Fatigue May Be Connected to Gut Bacteria among Young Physically Active Adults: An Exploratory Study. Nutrients 2022; 14:nu14030466. [PMID: 35276824 PMCID: PMC8839554 DOI: 10.3390/nu14030466] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Recent scientific evidence suggests that traits energy and fatigue are two unique unipolar moods with distinct mental and physical components. This exploratory study investigated the correlation between mental energy (ME), mental fatigue (MF), physical energy (PE), physical fatigue (PF), and the gut microbiome. The four moods were assessed by survey, and the gut microbiome and metabolome were determined from 16 S rRNA analysis and untargeted metabolomics analysis, respectively. Twenty subjects who were 31 ± 5 y, physically active, and not obese (26.4 ± 4.4 kg/m2) participated. Bacteroidetes (45%), the most prominent phyla, was only negatively correlated with PF. The second most predominant and butyrate-producing phyla, Firmicutes (43%), had members that correlated with each trait. However, the bacteria Anaerostipes was positively correlated with ME (0.048, p = 0.032) and negatively with MF (−0.532, p = 0.016) and PF (−0.448, p = 0.048), respectively. Diet influences the gut microbiota composition, and only one food group, processed meat, was correlated with the four moods—positively with MF (0.538, p = 0.014) and PF (0.513, p = 0.021) and negatively with ME (−0.790, p < 0.001) and PE (−0.478, p = 0.021). Only the Firmicutes genus Holdemania was correlated with processed meat (r = 0.488, p = 0.029). Distinct metabolic profiles were observed, yet these profiles were not significantly correlated with the traits. Study findings suggest that energy and fatigue are unique traits that could be defined by distinct bacterial communities not driven by diet. Larger studies are needed to confirm these exploratory findings.
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Affiliation(s)
- Ali Boolani
- Department of Physical Therapy, Clarkson University, Potsdam, NY 13699, USA
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
- Correspondence: (A.B.); (L.O.B.); Tel.: +504-319-5828 (A.B.); +704-340-4482 (L.O.B.)
| | - Karyn M. Gallivan
- Sports and Health Sciences, School of Health Sciences, American Public University System, Charles Town, WV 25414, USA; (K.M.G.); (K.S.O.)
| | - Kristin S. Ondrak
- Sports and Health Sciences, School of Health Sciences, American Public University System, Charles Town, WV 25414, USA; (K.M.G.); (K.S.O.)
| | - Courtney J. Christopher
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; (C.J.C.); (H.F.C.); (S.R.C.)
| | - Hector F. Castro
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; (C.J.C.); (H.F.C.); (S.R.C.)
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN 37996, USA
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; (C.J.C.); (H.F.C.); (S.R.C.)
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN 37996, USA
| | - Christopher M. Taylor
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (C.M.T.); (M.L.)
| | - Meng Luo
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (C.M.T.); (M.L.)
| | - Scot E. Dowd
- Molecular Research LP, 503 Clovis Rd, Shallowater, TX 79363, USA;
| | - Matthew Lee Smith
- Department of Environmental and Occupational Health, School of Public Health, Texas A&M University, College Station, TX 37916, USA;
- Center for Population Health and Aging, Texas A&M University, College Station, TX 77807, USA
| | - Lauri O. Byerley
- Sports and Health Sciences, School of Health Sciences, American Public University System, Charles Town, WV 25414, USA; (K.M.G.); (K.S.O.)
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- Correspondence: (A.B.); (L.O.B.); Tel.: +504-319-5828 (A.B.); +704-340-4482 (L.O.B.)
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18
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Santamaria G, Liao C, Lindberg C, Chen Y, Wang Z, Rhee K, Pinto FR, Yan J, Xavier JB. Evolution and regulation of microbial secondary metabolism. eLife 2022; 11:76119. [PMID: 36409069 PMCID: PMC9708071 DOI: 10.7554/elife.76119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large populations that collectively secrete massive amounts of secondary metabolites and alter their environment. Yet, the conditions favoring secondary metabolism despite the potential costs for primary metabolism remain unclear. Here we investigated the biosurfactants that the bacterium Pseudomonas aeruginosa makes and secretes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that the ability to make surfactants from glycerol varies inconsistently across the phylogenetic tree; instead, lineages that lost this ability are also worse at reducing the oxidative stress of primary metabolism on glycerol. Experiments with different carbon sources support a link with oxidative stress that explains the inconsistent distribution across the P. aeruginosa phylogeny and suggests a general principle: P. aeruginosa lineages produce surfactants if they can reduce the oxidative stress produced by primary metabolism and have excess resources, beyond their primary needs, to afford secondary metabolism. These results add a new layer to the regulation of a secondary metabolite unessential for primary metabolism but important to change physical properties of the environments surrounding bacterial populations.
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Affiliation(s)
- Guillem Santamaria
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States,BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Chloe Lindberg
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Zhe Wang
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Francisco Rodrigues Pinto
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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19
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Ye D, Li X, Shen J, Xia X. Microbial metabolomics: From novel technologies to diversified applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Optimization of metabolomic data processing using NOREVA. Nat Protoc 2022; 17:129-151. [PMID: 34952956 DOI: 10.1038/s41596-021-00636-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022]
Abstract
A typical output of a metabolomic experiment is a peak table corresponding to the intensity of measured signals. Peak table processing, an essential procedure in metabolomics, is characterized by its study dependency and combinatorial diversity. While various methods and tools have been developed to facilitate metabolomic data processing, it is challenging to determine which processing workflow will give good performance for a specific metabolomic study. NOREVA, an out-of-the-box protocol, was therefore developed to meet this challenge. First, the peak table is subjected to many processing workflows that consist of three to five defined calculations in combinatorially determined sequences. Second, the results of each workflow are judged against objective performance criteria. Third, various benchmarks are analyzed to highlight the uniqueness of this newly developed protocol in (1) evaluating the processing performance based on multiple criteria, (2) optimizing data processing by scanning thousands of workflows, and (3) allowing data processing for time-course and multiclass metabolomics. This protocol is implemented in an R package for convenient accessibility and to protect users' data privacy. Preliminary experience in R language would facilitate the usage of this protocol, and the execution time may vary from several minutes to a couple of hours depending on the size of the analyzed data.
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21
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Wang Q, Karvelsson ST, Johannsson F, Vilhjalmsson AI, Hagen L, de Miranda Fonseca D, Sharma A, Slupphaug G, Rolfsson O. UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines. Mol Oncol 2021; 16:1816-1840. [PMID: 34942055 PMCID: PMC9067156 DOI: 10.1002/1878-0261.13172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/04/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022] Open
Abstract
Metabolic rewiring is one of the indispensable drivers of epithelial-mesenchymal transition (EMT) involved in breast cancer metastasis. In this study, we explored the metabolic changes during spontaneous EMT in three separately established breast EMT cell models using a proteomics approach supported by metabolomic analysis. We identified common proteomic changes, including in the expression of CDH1, CDH2, VIM, LGALS1, SERPINE1, PKP3, ATP2A2, JUP, MTCH2, RPL26L1 and PLOD2. Consistently altered metabolic enzymes included: FDFT1, SORD, TSTA3 and UDP-glucose dehydrogenase (UGDH). Of these, UGDH was most prominently altered and has previously been associated with breast cancer patient survival. siRNA-mediated knockdown of UGDH resulted in delayed cell proliferation and dampened invasive potential of mesenchymal cells, and downregulated expression of the EMT transcription factor SNAI1. Metabolomic analysis revealed that siRNA-mediated knockdown of UGDH decreased intracellular glycerophosphocholine (GPC), whereas levels of acetylaspartate (NAA) increased. Finally, our data suggested that platelet-derived growth factor receptor beta (PDGFRB) signaling was activated in mesenchymal cells. siRNA-mediated knockdown of PDGFRB downregulated UGDH expression, potentially via NFkB-p65. Our results support an unexplored relationship between UGDH and GPC, both of which have previously been independently associated with breast cancer progression.
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Affiliation(s)
- Qiong Wang
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Sigurdur Trausti Karvelsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Freyr Johannsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Arnar Ingi Vilhjalmsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Davi de Miranda Fonseca
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Ottar Rolfsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
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22
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Hao D, Bai J, Du J, Wu X, Thomsen B, Gao H, Su G, Wang X. Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle. Metabolites 2021; 11:metabo11110753. [PMID: 34822411 PMCID: PMC8621036 DOI: 10.3390/metabo11110753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/23/2022] Open
Abstract
Metabolomics has been applied to measure the dynamic metabolic responses, to understand the systematic biological networks, to reveal the potential genetic architecture, etc., for human diseases and livestock traits. For example, the current published results include the detected relevant candidate metabolites, identified metabolic pathways, potential systematic networks, etc., for different cattle traits that can be applied for further metabolomic and integrated omics studies. Therefore, summarizing the applications of metabolomics for economic traits is required in cattle. We here provide a comprehensive review about metabolomic analysis and its integration with other omics in five aspects: (1) characterization of the metabolomic profile of cattle; (2) metabolomic applications in cattle; (3) integrated metabolomic analysis with other omics; (4) methods and tools in metabolomic analysis; and (5) further potentialities. The review aims to investigate the existing metabolomic studies by highlighting the results in cattle, integrated with other omics studies, to understand the metabolic mechanisms underlying the economic traits and to provide useful information for further research and practical breeding programs in cattle.
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Affiliation(s)
- Dan Hao
- Beijing Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Beijing 100193, China; (D.H.); (J.B.); (J.D.); (X.W.)
- Shijiazhuang Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Shijiazhuang 052463, China
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Jiangsong Bai
- Beijing Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Beijing 100193, China; (D.H.); (J.B.); (J.D.); (X.W.)
- Shijiazhuang Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Shijiazhuang 052463, China
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jianyong Du
- Beijing Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Beijing 100193, China; (D.H.); (J.B.); (J.D.); (X.W.)
- Shijiazhuang Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Shijiazhuang 052463, China
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaoping Wu
- Beijing Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Beijing 100193, China; (D.H.); (J.B.); (J.D.); (X.W.)
- Shijiazhuang Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd., Shijiazhuang 052463, China
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark; (H.G.); (G.S.)
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark; (H.G.); (G.S.)
| | - Xiao Wang
- Konge Larsen ApS, 2800 Kongens Lyngby, Denmark
- Correspondence:
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23
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Perspectives and challenges in extracellular vesicles untargeted metabolomics analysis. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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A hierarchical approach to removal of unwanted variation for large-scale metabolomics data. Nat Commun 2021; 12:4992. [PMID: 34404777 PMCID: PMC8371158 DOI: 10.1038/s41467-021-25210-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/23/2021] [Indexed: 01/13/2023] Open
Abstract
Liquid chromatography-mass spectrometry-based metabolomics studies are increasingly applied to large population cohorts, which run for several weeks or even years in data acquisition. This inevitably introduces unwanted intra- and inter-batch variations over time that can overshadow true biological signals and thus hinder potential biological discoveries. To date, normalisation approaches have struggled to mitigate the variability introduced by technical factors whilst preserving biological variance, especially for protracted acquisitions. Here, we propose a study design framework with an arrangement for embedding biological sample replicates to quantify variance within and between batches and a workflow that uses these replicates to remove unwanted variation in a hierarchical manner (hRUV). We use this design to produce a dataset of more than 1000 human plasma samples run over an extended period of time. We demonstrate significant improvement of hRUV over existing methods in preserving biological signals whilst removing unwanted variation for large scale metabolomics studies. Our tools not only provide a strategy for large scale data normalisation, but also provides guidance on the design strategy for large omics studies. Mass spectrometry-based metabolomics is a powerful method for profiling large clinical cohorts but batch variations can obscure biologically meaningful differences. Here, the authors develop a computational workflow that removes unwanted data variation while preserving biologically relevant information.
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25
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Harm T, Bild A, Dittrich K, Goldschmied A, Nestele J, Chatterjee M, Fu X, Kolb K, Castor T, Borst O, Geisler T, Rath D, LäMmerhofer M, Gawaz M. Acute coronary syndrome is associated with a substantial change in the platelet lipidome. Cardiovasc Res 2021; 118:1904-1916. [PMID: 34323932 DOI: 10.1093/cvr/cvab238] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/21/2021] [Indexed: 11/14/2022] Open
Abstract
AIMS Platelets play a key role in the pathophysiology of coronary artery disease (CAD) and patients with enhanced platelet activation are at increased risk to develop adverse cardiovascular events. Beyond reliable cardiovascular risk factors such as dyslipoproteinaemia, significant changes of platelet lipids occur in patients with CAD. In this study, we investigate the platelet lipidome by untargeted liquid chromatography-mass spectrometry, highlighting significant changes between acute coronary syndrome (ACS) and chronic coronary syndrome (CCS) patients. Additionally, we classify the platelet lipidome, spotlighting specific glycerophospholipids as key players in ACS patients. Furthermore, we examine the impact of significantly altered lipids in ACS on platelet-dependent thrombus formation and aggregation. METHODS AND RESULTS In this consecutive study, we characterized the platelet lipidome in a CAD cohort (n = 139) and showed significant changes of lipids between patients with ACS and CCS. We found that among 928 lipids, 7 platelet glycerophospholipids were significantly up-regulated in ACS, whereas 25 lipids were down-regulated compared to CCS. The most prominent up-regulated lipid in ACS, PC18:0 (PC 10:0-8:0), promoted platelet activation and ex vivo platelet-dependent thrombus formation. CONCLUSIONS Our results reveal that the platelet lipidome is altered in ACS and up-regulated lipids embody primarily glycerophospholipids. Alterations of the platelet lipidome, especially of medium chain lipids, may play a role in the pathophysiology of ACS.
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Affiliation(s)
- Tobias Harm
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Alexander Bild
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Kristina Dittrich
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Goldschmied
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Jeremy Nestele
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Madhumita Chatterjee
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Xiaoqing Fu
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Kyra Kolb
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Tatsiana Castor
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Oliver Borst
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Tobias Geisler
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Dominik Rath
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
| | - Michael LäMmerhofer
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, University Hospital Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
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26
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Yusifov A, Chhatre VE, Koplin EK, Wilson CE, Schmitt EE, Woulfe KC, Bruns DR. Transcriptomic analysis of cardiac gene expression across the life course in male and female mice. Physiol Rep 2021; 9:e14940. [PMID: 34245129 PMCID: PMC8271347 DOI: 10.14814/phy2.14940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Risk for heart disease increases with advanced age and differs between sexes, with females generally protected from heart disease until menopause. Despite these epidemiological observations, the molecular mechanisms that underlie sex‐specific differences in cardiac function have not been fully described. We used high throughput transcriptomics in juvenile (5 weeks), adult (4–6 months), and aged (18 months) male and female mice to understand how cardiac gene expression changes across the life course and by sex. While male gene expression profiles differed between juvenile‐adult and juvenile‐aged (254 and 518 genes, respectively), we found no significant differences in adult‐aged gene expression. Females had distinct gene expression changes across the life course with 1835 genes in juvenile‐adult and 1328 in adult‐aged. Analysis of differentially expressed genes (DEGs) suggests that juvenile to adulthood genes were clustered in cell cycle and development‐related pathways in contrast to adulthood‐aged which were characterized by immune‐and inflammation‐related pathways. Analysis of sex differences within each age suggests that juvenile and aged cardiac transcriptomes are different between males and females, with significantly fewer DEGs identified in adult males and females. Interestingly, the male–female differences in early age were distinct from those in advanced age. These findings are in contrast to expected sex differences historically attributed to estrogen and could not be explained by estrogen‐direct mechanisms alone as evidenced by juvenile sexual immaturity and reproductive incompetence in the aged mice. Together, distinct trajectories in cardiac transcriptomic profiles highlight fundamental sex differences across the life course and demonstrate the need for the consideration of age and sex as biological variables in heart disease.
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Affiliation(s)
- Aykhan Yusifov
- Kinesiology and Health, University of Wyoming, Laramie, WY, USA
| | | | - Eva K Koplin
- Kinesiology and Health, University of Wyoming, Laramie, WY, USA
| | - Cortney E Wilson
- Division of Cardiology, University of Colorado-Denver, Aurora, CO, USA
| | - Emily E Schmitt
- Kinesiology and Health, University of Wyoming, Laramie, WY, USA
| | - Kathleen C Woulfe
- Division of Cardiology, University of Colorado-Denver, Aurora, CO, USA.,Division of Geriatric Medicine, University of Colorado-Denver, Aurora, CO, USA
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27
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DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies. Sci Rep 2021; 11:5657. [PMID: 33707505 PMCID: PMC7952378 DOI: 10.1038/s41598-021-84824-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
As a powerful phenotyping technology, metabolomics provides new opportunities in biomarker discovery through metabolome-wide association studies (MWAS) and the identification of metabolites having a regulatory effect in various biological processes. While mass spectrometry-based (MS) metabolomics assays are endowed with high throughput and sensitivity, MWAS are doomed to long-term data acquisition generating an overtime-analytical signal drift that can hinder the uncovering of real biologically relevant changes. We developed “dbnorm”, a package in the R environment, which allows for an easy comparison of the model performance of advanced statistical tools commonly used in metabolomics to remove batch effects from large metabolomics datasets. “dbnorm” integrates advanced statistical tools to inspect the dataset structure not only at the macroscopic (sample batches) scale, but also at the microscopic (metabolic features) level. To compare the model performance on data correction, “dbnorm” assigns a score that help users identify the best fitting model for each dataset. In this study, we applied “dbnorm” to two large-scale metabolomics datasets as a proof of concept. We demonstrate that “dbnorm” allows for the accurate selection of the most appropriate statistical tool to efficiently remove the overtime signal drift and to focus on the relevant biological components of complex datasets.
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28
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Tripp BA, Dillon ST, Yuan M, Asara JM, Vasunilashorn SM, Fong TG, Metzger ED, Inouye SK, Xie Z, Ngo LH, Marcantonio ER, Libermann TA, Otu HH. Targeted metabolomics analysis of postoperative delirium. Sci Rep 2021; 11:1521. [PMID: 33452279 PMCID: PMC7810737 DOI: 10.1038/s41598-020-80412-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/15/2020] [Indexed: 01/29/2023] Open
Abstract
Postoperative delirium is the most common complication among older adults undergoing major surgery. The pathophysiology of delirium is poorly understood, and no blood-based, predictive markers are available. We characterized the plasma metabolome of 52 delirium cases and 52 matched controls from the Successful Aging after Elective Surgery (SAGES) cohort (N = 560) of patients ≥ 70 years old without dementia undergoing scheduled major non-cardiac surgery. We applied targeted mass spectrometry with internal standards and pooled controls using a nested matched case-control study preoperatively (PREOP) and on postoperative day 2 (POD2) to identify potential delirium risk and disease markers. Univariate analyses identified 37 PREOP and 53 POD2 metabolites associated with delirium and multivariate analyses achieved significant separation between the two groups with an 11-metabolite prediction model at PREOP (AUC = 83.80%). Systems biology analysis using the metabolites with differential concentrations rendered "valine, leucine, and isoleucine biosynthesis" at PREOP and "citrate cycle" at POD2 as the most significantly enriched pathways (false discovery rate < 0.05). Perturbations in energy metabolism and amino acid synthesis pathways may be associated with postoperative delirium and suggest potential mechanisms for delirium pathogenesis. Our results could lead to the development of a metabolomic delirium predictor.
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Affiliation(s)
- Bridget A. Tripp
- grid.24434.350000 0004 1937 0060Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Nebraska Hall E419, P.O. Box 880511, Lincoln, NE 68588 USA ,grid.24434.350000 0004 1937 0060PhD Program of Complex Biosystems, University of Nebraska-Lincoln, Lincoln, USA
| | - Simon T. Dillon
- grid.239395.70000 0000 9011 8547Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA
| | - Min Yuan
- grid.239395.70000 0000 9011 8547Division of Signal Transduction and Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, USA
| | - John M. Asara
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Division of Signal Transduction and Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, USA
| | - Sarinnapha M. Vasunilashorn
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA ,grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, USA
| | - Tamara G. Fong
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Neurology, Beth Israel Deaconess Medical Center, Boston, USA ,grid.38142.3c000000041936754XAging Brain Center, Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, USA
| | - Eran D. Metzger
- grid.38142.3c000000041936754XDepartment of Medicine, Hebrew SeniorLife, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, USA
| | - Sharon K. Inouye
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA ,grid.38142.3c000000041936754XAging Brain Center, Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, USA
| | - Zhongcong Xie
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.32224.350000 0004 0386 9924Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, USA
| | - Long H. Ngo
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA ,grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, USA
| | - Edward R. Marcantonio
- grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA
| | - Towia A. Libermann
- grid.239395.70000 0000 9011 8547Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, USA ,grid.239395.70000 0000 9011 8547Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA
| | - Hasan H. Otu
- grid.24434.350000 0004 1937 0060Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Nebraska Hall E419, P.O. Box 880511, Lincoln, NE 68588 USA
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29
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Mervant L, Tremblay-Franco M, Jamin EL, Kesse-Guyot E, Galan P, Martin JF, Guéraud F, Debrauwer L. Osmolality-based normalization enhances statistical discrimination of untargeted metabolomic urine analysis: results from a comparative study. Metabolomics 2021; 17:2. [PMID: 33389209 DOI: 10.1007/s11306-020-01758-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Because of its ease of collection, urine is one of the most commonly used matrices for metabolomics studies. However, unlike other biofluids, urine exhibits tremendous variability that can introduce confounding inconsistency during result interpretation. Despite many existing techniques to normalize urine samples, there is still no consensus on either which method is most appropriate or how to evaluate these methods. OBJECTIVES To investigate the impact of several methods and combinations of methods conventionally used in urine metabolomics on the statistical discrimination of two groups in a simple metabolomics study. METHODS We applied 14 different strategies of normalization to forty urine samples analysed by liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). To evaluate the impact of these different strategies, we relied on the ability of each method to reduce confounding variability while retaining variability of interest, as well as the predictability of statistical models. RESULTS Among all tested normalization methods, osmolality-based normalization gave the best results. Moreover, we demonstrated that normalization using a specific dilution prior to the analysis outperformed post-acquisition normalization. We also demonstrated that the combination of various normalization methods does not necessarily improve statistical discrimination. CONCLUSIONS This study re-emphasized the importance of normalizing urine samples for metabolomics studies. In addition, it appeared that the choice of method had a significant impact on result quality. Consequently, we suggest osmolality-based normalization as the best method for normalizing urine samples. TRIAL REGISTRATION NUMBER NCT03335644.
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Affiliation(s)
- Loïc Mervant
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Marie Tremblay-Franco
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France.
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.
| | - Emilien L Jamin
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Emmanuelle Kesse-Guyot
- Sorbonne Paris Nord University, Inserm, INRAE, Cnam, Nutritional Epidemiology, Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 93017, Bobigny, France
| | - Pilar Galan
- Sorbonne Paris Nord University, Inserm, INRAE, Cnam, Nutritional Epidemiology, Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 93017, Bobigny, France
| | - Jean-François Martin
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Françoise Guéraud
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Debrauwer
- Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
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30
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Yang Q, Hong J, Li Y, Xue W, Li S, Yang H, Zhu F. A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies. Brief Bioinform 2020; 21:2142-2152. [PMID: 31776543 PMCID: PMC7711263 DOI: 10.1093/bib/bbz137] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/26/2019] [Accepted: 10/05/2019] [Indexed: 12/19/2022] Open
Abstract
Unwanted experimental/biological variation and technical error are frequently encountered in current metabolomics, which requires the employment of normalization methods for removing undesired data fluctuations. To ensure the 'thorough' removal of unwanted variations, the collective consideration of multiple criteria ('intragroup variation', 'marker stability' and 'classification capability') was essential. However, due to the limited number of available normalization methods, it is extremely challenging to discover the appropriate one that can meet all these criteria. Herein, a novel approach was proposed to discover the normalization strategies that are consistently well performing (CWP) under all criteria. Based on various benchmarks, all normalization methods popular in current metabolomics were 'first' discovered to be non-CWP. 'Then', 21 new strategies that combined the 'sample'-based method with the 'metabolite'-based one were found to be CWP. 'Finally', a variety of currently available methods (such as cubic splines, range scaling, level scaling, EigenMS, cyclic loess and mean) were identified to be CWP when combining with other normalization. In conclusion, this study not only discovered several strategies that performed consistently well under all criteria, but also proposed a novel approach that could ensure the identification of CWP strategies for future biological problems.
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Affiliation(s)
- Qingxia Yang
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
| | - Jiajun Hong
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
| | - Yi Li
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
| | - Weiwei Xue
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
| | - Song Li
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
| | - Hui Yang
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
| | - Feng Zhu
- Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics
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31
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Bowerman KL, Rehman SF, Vaughan A, Lachner N, Budden KF, Kim RY, Wood DLA, Gellatly SL, Shukla SD, Wood LG, Yang IA, Wark PA, Hugenholtz P, Hansbro PM. Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nat Commun 2020; 11:5886. [PMID: 33208745 PMCID: PMC7676259 DOI: 10.1038/s41467-020-19701-0] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is the third commonest cause of death globally, and manifests as a progressive inflammatory lung disease with no curative treatment. The lung microbiome contributes to COPD progression, but the function of the gut microbiome remains unclear. Here we examine the faecal microbiome and metabolome of COPD patients and healthy controls, finding 146 bacterial species differing between the two groups. Several species, including Streptococcus sp000187445, Streptococcus vestibularis and multiple members of the family Lachnospiraceae, also correlate with reduced lung function. Untargeted metabolomics identifies a COPD signature comprising 46% lipid, 20% xenobiotic and 20% amino acid related metabolites. Furthermore, we describe a disease-associated network connecting Streptococcus parasanguinis_B with COPD-associated metabolites, including N-acetylglutamate and its analogue N-carbamoylglutamate. While correlative, our results suggest that the faecal microbiome and metabolome of COPD patients are distinct from those of healthy individuals, and may thus aid in the search for biomarkers for COPD. Chronic obstructive pulmonary disease (COPD) is a progressing disease, with lung but not gut microbiota implicated in its etiology. Here the authors compare the stool from patients with COPD and healthy controls to find specific gut bacteria and metabolites associated with active disease, thereby hinting at a potential role for the gut microbiome in COPD.
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Affiliation(s)
- Kate L Bowerman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Saima Firdous Rehman
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia
| | - Annalicia Vaughan
- Thoracic Research Centre, Faculty of Medicine, The University of Queensland, and Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Nancy Lachner
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kurtis F Budden
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia
| | - Richard Y Kim
- Centre for Inflammation, Centenary Institute & University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, Australia
| | - David L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia
| | - Shakti D Shukla
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia
| | - Lisa G Wood
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian A Yang
- Thoracic Research Centre, Faculty of Medicine, The University of Queensland, and Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Peter A Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, and The University of Newcastle, Newcastle, NSW, Australia. .,Centre for Inflammation, Centenary Institute & University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, Australia.
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32
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Plyushchenko I, Shakhmatov D, Bolotnik T, Baygildiev T, Nesterenko PN, Rodin I. An approach for feature selection with data modelling in LC-MS metabolomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3582-3591. [PMID: 32701078 DOI: 10.1039/d0ay00204f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The data processing workflow for LC-MS based metabolomics study is suggested with signal drift correction, univariate analysis, supervised learning, feature selection and unsupervised modelling. The proposed approach requires only an annotation-free peak table and produces an extremely reduced set of the most relevant features together with validation via Receiver Operating Characteristic analysis for selected predictors, cross-validation and unsupervised projection. The presented study was initially optimised by its own experimental set and then was successfully tested by using 36 datasets from 21 publicly available metabolomics projects. The suggested workflow can be used for classification purposes in high dimensional metabolomics studies and as a first step in exploratory analysis, data projection, biomarker selection, data integration and fusion.
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Affiliation(s)
- Ivan Plyushchenko
- Lomonosov Moscow State University, Chemistry Department, 119992, GSP-2, Lenin Hills, 1b3, Moscow, Russia.
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Yang Q, Wang Y, Zhang Y, Li F, Xia W, Zhou Y, Qiu Y, Li H, Zhu F. NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data. Nucleic Acids Res 2020; 48:W436-W448. [PMID: 32324219 PMCID: PMC7319444 DOI: 10.1093/nar/gkaa258] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/21/2020] [Accepted: 04/04/2020] [Indexed: 12/23/2022] Open
Abstract
Biological processes (like microbial growth & physiological response) are usually dynamic and require the monitoring of metabolic variation at different time-points. Moreover, there is clear shift from case-control (N=2) study to multi-class (N>2) problem in current metabolomics, which is crucial for revealing the mechanisms underlying certain physiological process, disease metastasis, etc. These time-course and multi-class metabolomics have attracted great attention, and data normalization is essential for removing unwanted biological/experimental variations in these studies. However, no tool (including NOREVA 1.0 focusing only on case-control studies) is available for effectively assessing the performance of normalization method on time-course/multi-class metabolomic data. Thus, NOREVA was updated to version 2.0 by (i) realizing normalization and evaluation of both time-course and multi-class metabolomic data, (ii) integrating 144 normalization methods of a recently proposed combination strategy and (iii) identifying the well-performing methods by comprehensively assessing the largest set of normalizations (168 in total, significantly larger than those 24 in NOREVA 1.0). The significance of this update was extensively validated by case studies on benchmark datasets. All in all, NOREVA 2.0 is distinguished for its capability in identifying well-performing normalization method(s) for time-course and multi-class metabolomics, which makes it an indispensable complement to other available tools. NOREVA can be accessed at https://idrblab.org/noreva/.
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Affiliation(s)
- Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation & The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation & The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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34
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Misra BB. Data normalization strategies in metabolomics: Current challenges, approaches, and tools. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:165-174. [PMID: 32276547 DOI: 10.1177/1469066720918446] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Data normalization is a big challenge in quantitative metabolomics approaches, whether targeted or untargeted. Without proper normalization, the mass-spectrometry and spectroscopy data can provide erroneous, sub-optimal data, which can lead to misleading and confusing biological results and thereby result in failed application to human healthcare, clinical, and other research avenues. To address this issue, a number of statistical approaches and software tools have been proposed in the literature and implemented over the years, thereby providing a multitude of approaches to choose from - either sample-based or data-based normalization strategies. In recent years, new dedicated software tools for metabolomics data normalization have surfaced as well. In this account article, I summarize the existing approaches and the new discoveries and research findings in this area of metabolomics data normalization, and I introduce some recent tools that aid in data normalization.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Section of Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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35
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Data-dependent normalization strategies for untargeted metabolomics—a case study. Anal Bioanal Chem 2020; 412:6391-6405. [DOI: 10.1007/s00216-020-02594-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022]
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36
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Fernández-Ochoa Á, Quirantes-Piné R, Borrás-Linares I, Cádiz-Gurrea MDLL, Alarcón Riquelme ME, Brunius C, Segura-Carretero A. A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics. Metabolites 2020; 10:metabo10010028. [PMID: 31936230 PMCID: PMC7022532 DOI: 10.3390/metabo10010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/01/2020] [Accepted: 01/06/2020] [Indexed: 12/21/2022] Open
Abstract
Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more effectively correct the drifts due to between and within batch effects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining different packages, functions, and methods in a single environment.
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Affiliation(s)
- Álvaro Fernández-Ochoa
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av Fuentenueva s/n, 18071 Granada, Spain;
- Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Av del Conocimiento, No. 37, s/n, 18016 Granada, Spain; (R.Q.-P.); (I.B.-L.)
- Correspondence: (Á.F.-O.); (M.d.l.L.C.-G.); (C.B.); Tel.: +34-958-637-206 (Á.F.-O.)
| | - Rosa Quirantes-Piné
- Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Av del Conocimiento, No. 37, s/n, 18016 Granada, Spain; (R.Q.-P.); (I.B.-L.)
| | - Isabel Borrás-Linares
- Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Av del Conocimiento, No. 37, s/n, 18016 Granada, Spain; (R.Q.-P.); (I.B.-L.)
| | - María de la Luz Cádiz-Gurrea
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av Fuentenueva s/n, 18071 Granada, Spain;
- Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Av del Conocimiento, No. 37, s/n, 18016 Granada, Spain; (R.Q.-P.); (I.B.-L.)
- Correspondence: (Á.F.-O.); (M.d.l.L.C.-G.); (C.B.); Tel.: +34-958-637-206 (Á.F.-O.)
| | | | - Marta E. Alarcón Riquelme
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Government, Health Science Technological Park, Av de la Ilustración 114, 18016 Granada, Spain;
| | - Carl Brunius
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Correspondence: (Á.F.-O.); (M.d.l.L.C.-G.); (C.B.); Tel.: +34-958-637-206 (Á.F.-O.)
| | - Antonio Segura-Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av Fuentenueva s/n, 18071 Granada, Spain;
- Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Av del Conocimiento, No. 37, s/n, 18016 Granada, Spain; (R.Q.-P.); (I.B.-L.)
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37
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Pittard WS, Villaveces CK, Li S. A Bioinformatics Primer to Data Science, with Examples for Metabolomics. Methods Mol Biol 2020; 2104:245-263. [PMID: 31953822 DOI: 10.1007/978-1-0716-0239-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
With the increasing importance of big data in biomedicine, skills in data science are a foundation for the individual career development and for the progress of science. This chapter is a practical guide to working with high-throughput biomedical data. It covers how to understand and set up the computing environment, to start a research project with proper and effective data management, and to perform common bioinformatics tasks such as data wrangling, quality control, statistical analysis, and visualization, with examples on metabolomics data. Concepts and tools related to coding and scripting are discussed. Version control, knitr and Jupyter notebooks are important to project management, collaboration, and research reproducibility. Overall, this chapter describes a core set of skills to work in bioinformatics, and can serve as a reference text at the level of a graduate course and interfacing with data science.
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Affiliation(s)
- W Stephen Pittard
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Shuzhao Li
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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38
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González-Riano C, Dudzik D, Garcia A, Gil-de-la-Fuente A, Gradillas A, Godzien J, López-Gonzálvez Á, Rey-Stolle F, Rojo D, Ruperez FJ, Saiz J, Barbas C. Recent Developments along the Analytical Process for Metabolomics Workflows. Anal Chem 2019; 92:203-226. [PMID: 31625723 DOI: 10.1021/acs.analchem.9b04553] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Carolina González-Riano
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Danuta Dudzik
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain.,Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy , Medical University of Gdańsk , 80-210 Gdańsk , Poland
| | - Antonia Garcia
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Alberto Gil-de-la-Fuente
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU , 28003 Madrid , Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain.,Clinical Research Centre , Medical University of Bialystok , 15-089 Bialystok , Poland
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Francisco J Ruperez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Jorge Saiz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
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39
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Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites 2019; 9:E200. [PMID: 31548506 PMCID: PMC6835268 DOI: 10.3390/metabo9100200] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022] Open
Abstract
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.
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Affiliation(s)
- Jan Stanstrup
- Preventive and Clinical Nutrition, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark.
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany.
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
| | - Luca Nicolotti
- The Australian Wine Research Institute, Metabolomics Australia, PO Box 197, Adelaide SA 5064, Australia.
| | - Kristian Peters
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.
| | - Reza M Salek
- The International Agency for Research on Cancer, 150 cours Albert Thomas, CEDEX 08, 69372 Lyon, France.
| | - Tobias Schulze
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg.
| | - Michael A Stravs
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dubendorf, Switzerland.
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Sciences and Decision, MetaboHUB, Gif-Sur-Yvette F-91191, France.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Ralf J M Weber
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
- Chair of Analytical Food Chemistry, Technische Universität München, 85354 Weihenstephan, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig Deutscher, Platz 5e, 04103 Leipzig, Germany.
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Mack CI, Egert B, Liberto E, Weinert CH, Bub A, Hoffmann I, Bicchi C, Kulling SE, Cordero C. Robust Markers of Coffee Consumption Identified Among the Volatile Organic Compounds in Human Urine. Mol Nutr Food Res 2019; 63:e1801060. [DOI: 10.1002/mnfr.201801060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/15/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Carina I. Mack
- Max Rubner‐InstitutDepartment of Safety and Quality of Fruit and Vegetables Haid‐und‐Neu‐Straße 9 76131 Karlsruhe Germany
| | - Björn Egert
- Max Rubner‐InstitutDepartment of Safety and Quality of Fruit and Vegetables Haid‐und‐Neu‐Straße 9 76131 Karlsruhe Germany
| | - Erica Liberto
- Università degli Studi di TorinoDipartimento di Scienza e tecnologia del Farmaco Via Pietro Giuria 9 10125 Torino Italy
| | - Christoph H. Weinert
- Max Rubner‐InstitutDepartment of Safety and Quality of Fruit and Vegetables Haid‐und‐Neu‐Straße 9 76131 Karlsruhe Germany
| | - Achim Bub
- Max Rubner‐InstitutDepartment of Physiology and Biochemistry of Nutrition Haid‐und‐Neu‐Straße 9 76131 Karlsruhe Germany
| | - Ingrid Hoffmann
- Max Rubner‐InstitutDepartment of Nutritional Behaviour Haid‐und‐Neu‐Straße 9 76131 Karlsruhe Germany
| | - Carlo Bicchi
- Università degli Studi di TorinoDipartimento di Scienza e tecnologia del Farmaco Via Pietro Giuria 9 10125 Torino Italy
| | - Sabine E. Kulling
- Max Rubner‐InstitutDepartment of Safety and Quality of Fruit and Vegetables Haid‐und‐Neu‐Straße 9 76131 Karlsruhe Germany
| | - Chiara Cordero
- Università degli Studi di TorinoDipartimento di Scienza e tecnologia del Farmaco Via Pietro Giuria 9 10125 Torino Italy
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Stratton KG, Webb-Robertson BJM, McCue LA, Stanfill B, Claborne D, Godinez I, Johansen T, Thompson AM, Burnum-Johnson KE, Waters KM, Bramer LM. pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data. J Proteome Res 2019; 18:1418-1425. [PMID: 30638385 PMCID: PMC6750869 DOI: 10.1021/acs.jproteome.8b00760] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Prior
to statistical analysis of mass spectrometry (MS) data, quality
control (QC) of the identified biomolecule peak intensities is imperative
for reducing process-based sources of variation and extreme biological
outliers. Without this step, statistical results can be biased. Additionally,
liquid chromatography–MS proteomics data present inherent challenges
due to large amounts of missing data that require special consideration
during statistical analysis. While a number of R packages exist to
address these challenges individually, there is no single R package
that addresses all of them. We present pmartR, an
open-source R package, for QC (filtering and normalization), exploratory
data analysis (EDA), visualization, and statistical analysis robust
to missing data. Example analysis using proteomics data from a mouse
study comparing smoke exposure to control demonstrates the core functionality
of the package and highlights the capabilities for handling missing
data. In particular, using a combined quantitative and qualitative
statistical test, 19 proteins whose statistical significance would
have been missed by a quantitative test alone were identified. The pmartR package provides a single software tool for QC, EDA,
and statistical comparisons of MS data that is robust to missing data
and includes numerous visualization capabilities.
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Affiliation(s)
- Kelly G Stratton
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Bobbie-Jo M Webb-Robertson
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Lee Ann McCue
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Bryan Stanfill
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Daniel Claborne
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Iobani Godinez
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Thomas Johansen
- Department of Statistics , Florida State University , 117 North Woodward Avenue , Tallahassee , Florida 32306 , United States
| | - Allison M Thompson
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Kristin E Burnum-Johnson
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Katrina M Waters
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Lisa M Bramer
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
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42
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Misra BB, Mohapatra S. Tools and resources for metabolomics research community: A 2017-2018 update. Electrophoresis 2018; 40:227-246. [PMID: 30443919 DOI: 10.1002/elps.201800428] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023]
Abstract
The scale at which MS- and NMR-based platforms generate metabolomics datasets for both research, core, and clinical facilities to address challenges in the various sciences-ranging from biomedical to agricultural-is underappreciated. Thus, metabolomics efforts spanning microbe, environment, plant, animal, and human systems have led to continual and concomitant growth of in silico resources for analysis and interpretation of these datasets. These software tools, resources, and databases drive the field forward to help keep pace with the amount of data being generated and the sophisticated and diverse analytical platforms that are being used to generate these metabolomics datasets. To address challenges in data preprocessing, metabolite annotation, statistical interrogation, visualization, interpretation, and integration, the metabolomics and informatics research community comes up with hundreds of tools every year. The purpose of the present review is to provide a brief and useful summary of more than 95 metabolomics tools, software, and databases that were either developed or significantly improved during 2017-2018. We hope to see this review help readers, developers, and researchers to obtain informed access to these thorough lists of resources for further improvisation, implementation, and application in due course of time.
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Affiliation(s)
- Biswapriya B Misra
- Department of Internal Medicine, Section of Molecular Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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43
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Zacharias HU, Altenbuchinger M, Gronwald W. Statistical Analysis of NMR Metabolic Fingerprints: Established Methods and Recent Advances. Metabolites 2018; 8:E47. [PMID: 30154338 PMCID: PMC6161311 DOI: 10.3390/metabo8030047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/01/2018] [Accepted: 08/18/2018] [Indexed: 01/02/2023] Open
Abstract
In this review, we summarize established and recent bioinformatic and statistical methods for the analysis of NMR-based metabolomics. Data analysis of NMR metabolic fingerprints exhibits several challenges, including unwanted biases, high dimensionality, and typically low sample numbers. Common analysis tasks comprise the identification of differential metabolites and the classification of specimens. However, analysis results strongly depend on the preprocessing of the data, and there is no consensus yet on how to remove unwanted biases and experimental variance prior to statistical analysis. Here, we first review established and new preprocessing protocols and illustrate their pros and cons, including different data normalizations and transformations. Second, we give a brief overview of state-of-the-art statistical analysis in NMR-based metabolomics. Finally, we discuss a recent development in statistical data analysis, where data normalization becomes obsolete. This method, called zero-sum regression, builds metabolite signatures whose estimation as well as predictions are independent of prior normalization.
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Affiliation(s)
- Helena U Zacharias
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Michael Altenbuchinger
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Am Biopark 9, 93053 Regensburg, Germany.
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Am Biopark 9, 93053 Regensburg, Germany.
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