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Nikulkova M, Abdrabou W, Carlton JM, Idaghdour Y. Exploiting integrative metabolomics to study host-parasite interactions in Plasmodium infections. Trends Parasitol 2024; 40:313-323. [PMID: 38508901 PMCID: PMC10994734 DOI: 10.1016/j.pt.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Despite years of research, malaria remains a significant global health burden, with poor diagnostic tests and increasing antimalarial drug resistance challenging diagnosis and treatment. While 'single-omics'-based approaches have been instrumental in gaining insight into the biology and pathogenicity of the Plasmodium parasite and its interaction with the human host, a more comprehensive understanding of malaria pathogenesis can be achieved through 'multi-omics' approaches. Integrative methods, which combine metabolomics, lipidomics, transcriptomics, and genomics datasets, offer a holistic systems biology approach to studying malaria. This review highlights recent advances, future directions, and challenges involved in using integrative metabolomics approaches to interrogate the interactions between Plasmodium and the human host, paving the way towards targeted antimalaria therapeutics and control intervention methods.
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Affiliation(s)
- Maria Nikulkova
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 11101, USA; Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Wael Abdrabou
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 11101, USA; Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
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2
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Xu T, Jiang Y, Fu H, Yang G, Hu X, Chen Y, Zhang Q, Wang Y, Wang Y, Xie HQ, Han F, Xu L, Zhao B. Exploring the adverse effects of 1,3,6,8-tetrabromo-9H-carbazole in atherosclerotic model mice by metabolomic profiling integrated with mechanism studies in vitro. CHEMOSPHERE 2024; 349:140767. [PMID: 37992903 DOI: 10.1016/j.chemosphere.2023.140767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Given its wide distribution in the environment and latent toxic effects, 1,3,6,8-tetrabromo-9H-carbazole (1368-BCZ) is an emerging concern that has gained increasing attention globally. 1368-BCZ exposure is reported to have potential cardiovascular toxicity. Although atherosclerosis is a cardiovascular disease and remains a primary cause of mortality worldwide, no evidence has been found regarding the impact of 1368-BCZ on atherosclerosis. Therefore, we aimed to explore the deleterious effects of 1368-BCZ on atherosclerosis and the underlying mechanisms. Serum samples from 1368-BCZ-treated atherosclerotic model mice were subjected to metabolomic profiling to investigate the adverse influence of the pollutant. Subsequently, the molecular mechanism associated with the metabolic pathway of atherosclerotic mice that was identified following 1368-BCZ exposure was validated in vitro. Serum metabolomics analysis revealed that 1368-BCZ significantly altered the tricarboxylic acid cycle, causing a disturbance in energy metabolism. In vitro, we further validated general markers of energy metabolism based on metabolome data: 1368-BCZ dampened adenosine triphosphate (ATP) synthesis and increased reactive oxygen species (ROS) production. Furthermore, blocking the aryl hydrocarbon receptor (AhR) reversed the high production of ROS induced by 1368-BCZ. It is concluded that 1368-BCZ decreased the ATP synthesis by disturbing the energy metabolism, thereby stimulating the AhR-mediated ROS production and presumably causing aggravated atherosclerosis. This is the first comprehensive study on the cardiovascular toxicity and mechanism of 1368-BCZ based on rodent models of atherosclerosis and integrated with in vitro models.
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Affiliation(s)
- Tong Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; PET/CT Center, Key Laboratory of Functional Molecular Imaging, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China
| | - Yu Jiang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Hualing Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guanglei Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxu Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangsheng Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Zhang
- Department of Cardiology, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
| | - Yuxi Wang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Yilan Wang
- PET/CT Center, Key Laboratory of Functional Molecular Imaging, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China
| | - Heidi Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Han
- PET/CT Center, Key Laboratory of Functional Molecular Imaging, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China.
| | - Li Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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3
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Fernandez ME, Martinez-Romero J, Aon MA, Bernier M, Price NL, de Cabo R. How is Big Data reshaping preclinical aging research? Lab Anim (NY) 2023; 52:289-314. [PMID: 38017182 DOI: 10.1038/s41684-023-01286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
The exponential scientific and technological progress during the past 30 years has favored the comprehensive characterization of aging processes with their multivariate nature, leading to the advent of Big Data in preclinical aging research. Spanning from molecular omics to organism-level deep phenotyping, Big Data demands large computational resources for storage and analysis, as well as new analytical tools and conceptual frameworks to gain novel insights leading to discovery. Systems biology has emerged as a paradigm that utilizes Big Data to gain insightful information enabling a better understanding of living organisms, visualized as multilayered networks of interacting molecules, cells, tissues and organs at different spatiotemporal scales. In this framework, where aging, health and disease represent emergent states from an evolving dynamic complex system, context given by, for example, strain, sex and feeding times, becomes paramount for defining the biological trajectory of an organism. Using bioinformatics and artificial intelligence, the systems biology approach is leading to remarkable advances in our understanding of the underlying mechanism of aging biology and assisting in creative experimental study designs in animal models. Future in-depth knowledge acquisition will depend on the ability to fully integrate information from different spatiotemporal scales in organisms, which will probably require the adoption of theories and methods from the field of complex systems. Here we review state-of-the-art approaches in preclinical research, with a focus on rodent models, that are leading to conceptual and/or technical advances in leveraging Big Data to understand basic aging biology and its full translational potential.
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Affiliation(s)
- Maria Emilia Fernandez
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jorge Martinez-Romero
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Miguel A Aon
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Michel Bernier
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nathan L Price
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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Lakhani A, Kang DH, Kang YE, Park JO. Toward Systems-Level Metabolic Analysis in Endocrine Disorders and Cancer. Endocrinol Metab (Seoul) 2023; 38:619-630. [PMID: 37989266 PMCID: PMC10764991 DOI: 10.3803/enm.2023.1814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023] Open
Abstract
Metabolism is a dynamic network of biochemical reactions that support systemic homeostasis amidst changing nutritional, environmental, and physical activity factors. The circulatory system facilitates metabolite exchange among organs, while the endocrine system finely tunes metabolism through hormone release. Endocrine disorders like obesity, diabetes, and Cushing's syndrome disrupt this balance, contributing to systemic inflammation and global health burdens. They accompany metabolic changes on multiple levels from molecular interactions to individual organs to the whole body. Understanding how metabolic fluxes relate to endocrine disorders illuminates the underlying dysregulation. Cancer is increasingly considered a systemic disorder because it not only affects cells in localized tumors but also the whole body, especially in metastasis. In tumorigenesis, cancer-specific mutations and nutrient availability in the tumor microenvironment reprogram cellular metabolism to meet increased energy and biosynthesis needs. Cancer cachexia results in metabolic changes to other organs like muscle, adipose tissue, and liver. This review explores the interplay between the endocrine system and systems-level metabolism in health and disease. We highlight metabolic fluxes in conditions like obesity, diabetes, Cushing's syndrome, and cancers. Recent advances in metabolomics, fluxomics, and systems biology promise new insights into dynamic metabolism, offering potential biomarkers, therapeutic targets, and personalized medicine.
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Affiliation(s)
- Aliya Lakhani
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Da Hyun Kang
- Department of Internal Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Yea Eun Kang
- Department of Internal Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Junyoung O. Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
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5
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Mollova D, Gozmanova M, Apostolova E, Yahubyan G, Iliev I, Baev V. Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3-A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing. Microorganisms 2023; 11:2440. [PMID: 37894099 PMCID: PMC10609609 DOI: 10.3390/microorganisms11102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Lactiplantibacillus plantarum stands out as a remarkably diverse species of lactic acid bacteria, occupying a myriad of ecological niches. Particularly noteworthy is its presence in human breast milk, which can serve as a reservoir of probiotic bacteria, contributing significantly to the establishment and constitution of infant gut microbiota. In light of this, our study attempted to conduct an initial investigation encompassing both genomic and phenotypic aspects of the L. plantarum PU3 strain, that holds potential as a probiotic agent. By employing the cutting-edge third-generation Nanopore sequencing technology, L. plantarum PU3 revealed a circular chromosome of 3,180,940 bp and nine plasmids of various lengths. The L. plantarum PU3 genome has a total of 2962 protein-coding and non-coding genes. Our in-depth investigations revealed more than 150 probiotic gene markers that unfold the genetic determinants for acid tolerance, bile resistance, adhesion, and oxidative and osmotic stress. The in vivo analysis showed the strain's proficiency in utilizing various carbohydrates as growth substrates, complementing the in silico analysis of the genes involved in metabolic pathways. Notably, the strain demonstrated a pronounced affinity for D-sorbitol, D-mannitol, and D-Gluconic acid, among other carbohydrate sources. The in vitro experimental verification of acid, osmotic and bile tolerance validated the robustness of the strain in challenging environments. Encouragingly, no virulence factors were detected in the genome of PU3, suggesting its safety profile. In search of beneficial properties, we found potential bacteriocin biosynthesis clusters, suggesting its capability for antimicrobial activity. The characteristics exhibited by L. plantarum PU3 pave the way for promising strain potential, warranting further investigations to unlock its full capacity and contributions to probiotic and therapeutic avenues.
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Affiliation(s)
- Daniela Mollova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Mariyana Gozmanova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Elena Apostolova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Ilia Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
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6
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Microbiome and Metabolomics in Liver Cancer: Scientific Technology. Int J Mol Sci 2022; 24:ijms24010537. [PMID: 36613980 PMCID: PMC9820585 DOI: 10.3390/ijms24010537] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Primary liver cancer is a heterogeneous disease. Liver cancer metabolism includes both the reprogramming of intracellular metabolism to enable cancer cells to proliferate inappropriately and adapt to the tumor microenvironment and fluctuations in regular tissue metabolism. Currently, metabolomics and metabolite profiling in liver cirrhosis, liver cancer, and hepatocellular carcinoma (HCC) have been in the spotlight in terms of cancer diagnosis, monitoring, and therapy. Metabolomics is the global analysis of small molecules, chemicals, and metabolites. Metabolomics technologies can provide critical information about the liver cancer state. Here, we review how liver cirrhosis, liver cancer, and HCC therapies interact with metabolism at the cellular and systemic levels. An overview of liver metabolomics is provided, with a focus on currently available technologies and how they have been used in clinical and translational research. We also list scalable methods, including chemometrics, followed by pathway processing in liver cancer. We conclude that important drivers of metabolomics science and scientific technologies are novel therapeutic tools and liver cancer biomarker analysis.
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7
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Rinschen MM, Harder JL, Carter-Timofte ME, Zanon Rodriguez L, Mirabelli C, Demir F, Kurmasheva N, Ramakrishnan SK, Kunke M, Tan Y, Billing A, Dahlke E, Larionov AA, Bechtel-Walz W, Aukschun U, Grabbe M, Nielsen R, Christensen EI, Kretzler M, Huber TB, Wobus CE, Olagnier D, Siuzdak G, Grahammer F, Theilig F. VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney. Sci Signal 2022; 15:eabo7940. [PMID: 36445937 PMCID: PMC10350314 DOI: 10.1126/scisignal.abo7940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The lipid kinase VPS34 orchestrates autophagy, endocytosis, and metabolism and is implicated in cancer and metabolic disease. The proximal tubule in the kidney is a key metabolic organ that controls reabsorption of nutrients such as fatty acids, amino acids, sugars, and proteins. Here, by combining metabolomics, proteomics, and phosphoproteomics analyses with functional and superresolution imaging assays of mice with an inducible deficiency in proximal tubular cells, we revealed that VPS34 controlled the metabolome of the proximal tubule. In addition to inhibiting pinocytosis and autophagy, VPS34 depletion induced membrane exocytosis and reduced the abundance of the retromer complex necessary for proper membrane recycling and lipid retention, leading to a loss of fuel and biomass. Integration of omics data into a kidney cell metabolomic model demonstrated that VPS34 deficiency increased β-oxidation, reduced gluconeogenesis, and enhanced the use of glutamine for energy consumption. Furthermore, the omics datasets revealed that VPS34 depletion triggered an antiviral response that included a decrease in the abundance of apically localized virus receptors such as ACE2. VPS34 inhibition abrogated SARS-CoV-2 infection in human kidney organoids and cultured proximal tubule cells in a glutamine-dependent manner. Thus, our results demonstrate that VPS34 adjusts endocytosis, nutrient transport, autophagy, and antiviral responses in proximal tubule cells in the kidney.
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Affiliation(s)
- Markus M Rinschen
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA 92037, USA
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, 50937 Cologne, Germany
- Aarhus Institute for Advanced Studies, Aarhus University, 8000 Aarhus, Denmark
| | - Jennifer L Harder
- Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Fatih Demir
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | | | - Madlen Kunke
- Department of Anatomy, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Yifan Tan
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Anja Billing
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Eileen Dahlke
- Department of Anatomy, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Alexey A Larionov
- Department of Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Wibke Bechtel-Walz
- IV Department of Medicine and Faculty of Medicine, University Medical Center Freiburg, 79110 Freiburg, Germany
| | - Ute Aukschun
- IV Department of Medicine and Faculty of Medicine, University Medical Center Freiburg, 79110 Freiburg, Germany
| | - Marlen Grabbe
- IV Department of Medicine and Faculty of Medicine, University Medical Center Freiburg, 79110 Freiburg, Germany
| | - Rikke Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David Olagnier
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Gary Siuzdak
- Scripps Center for Metabolomics, Scripps Research, La Jolla, CA 92037, USA
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Franziska Theilig
- Department of Anatomy, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
- Department of Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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8
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Guignard D, Canlet C, Tremblay-Franco M, Chaillou E, Gautier R, Gayrard V, Picard-Hagen N, Schroeder H, Jourdan F, Zalko D, Viguié C, Cabaton NJ. Gestational exposure to bisphenol A induces region-specific changes in brain metabolomic fingerprints in sheep. ENVIRONMENT INTERNATIONAL 2022; 165:107336. [PMID: 35700571 DOI: 10.1016/j.envint.2022.107336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Fetal brain development depends on maternofetal thyroid function. In rodents and sheep, perinatal BPA exposure is associated with maternal and/or fetal thyroid disruption and alterations in central nervous system development as demonstrated by metabolic modulations in the encephala of mice. We hypothesized that a gestational exposure to a low dose of BPA affects maternofetal thyroid function and fetal brain development in a region-specific manner. Pregnant ewes, a relevant model for human thyroid and brain development, were exposed to BPA (5 µg/kg bw/d, sc). The thyroid status of ewes during gestation and term fetuses at delivery was monitored. Fetal brain development was assessed by metabolic fingerprints at birth in 10 areas followed by metabolic network-based analysis. BPA treatment was associated with a significant time-dependent decrease in maternal TT4 serum concentrations. For 8 fetal brain regions, statistical models allowed discriminating BPA-treated from control lambs. Metabolic network computational analysis revealed that prenatal exposure to BPA modulated several metabolic pathways, in particular excitatory and inhibitory amino-acid, cholinergic, energy and lipid homeostasis pathways. These pathways might contribute to BPA-related neurobehavioral and cognitive disorders. Discrimination was particularly clear for the dorsal hippocampus, the cerebellar vermis, the dorsal hypothalamus, the caudate nucleus and the lateral part of the frontal cortex. Compared with previous results in rodents, the use of a larger animal model allowed to examine specific brain areas, and generate evidence of the distinct region-specific effects of fetal BPA exposure on the brain metabolome. These modifications occur concomitantly to subtle maternal thyroid function alteration. The functional link between such moderate thyroid changes and fetal brain metabolomic fingerprints remains to be determined as well as the potential implication of other modes of action triggered by BPA such as estrogenic ones. Our results pave the ways for new scientific strategies aiming at linking environmental endocrine disruption and altered neurodevelopment.
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Affiliation(s)
- Davy Guignard
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, Toulouse, France
| | - Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, Toulouse, France
| | - Elodie Chaillou
- CNRS, IFCE, INRAE, Université de Tours, PRC, Nouzilly, France
| | - Roselyne Gautier
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, Toulouse, France
| | - Véronique Gayrard
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nicole Picard-Hagen
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Henri Schroeder
- Université de Lorraine, INSERM U1256, NGERE, Nutrition Génétique et Exposition aux Risques Environnementaux, 54000 Nancy, France
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Daniel Zalko
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Catherine Viguié
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.
| | - Nicolas J Cabaton
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
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9
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Dussarrat T, Prigent S, Latorre C, Bernillon S, Flandin A, Díaz FP, Cassan C, Van Delft P, Jacob D, Varala K, Joubes J, Gibon Y, Rolin D, Gutiérrez RA, Pétriacq P. Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. THE NEW PHYTOLOGIST 2022; 234:1614-1628. [PMID: 35288949 PMCID: PMC9324839 DOI: 10.1111/nph.18095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.
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Affiliation(s)
- Thomas Dussarrat
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
| | - Sylvain Prigent
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Claudio Latorre
- Departamento de EcologíaPontificia Universidad Católica de ChileAv Libertador Bernardo O'Higgins 340SantiagoChile
- Institute of Ecology and Biodiversity (IEB)Las Palmeras3425ÑuñoaSantiagoChile
| | - Stéphane Bernillon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Amélie Flandin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Francisca P. Díaz
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Cédric Cassan
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Pierre Van Delft
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Daniel Jacob
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Kranthi Varala
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Jérôme Joubes
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Yves Gibon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Dominique Rolin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Rodrigo A. Gutiérrez
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Pierre Pétriacq
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
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10
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Wandy J, Daly R. GraphOmics: an interactive platform to explore and integrate multi-omics data. BMC Bioinformatics 2021; 22:603. [PMID: 34922446 PMCID: PMC8684259 DOI: 10.1186/s12859-021-04500-1] [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: 06/23/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND An increasing number of studies now produce multiple omics measurements that require using sophisticated computational methods for analysis. While each omics data can be examined separately, jointly integrating multiple omics data allows for deeper understanding and insights to be gained from the study. In particular, data integration can be performed horizontally, where biological entities from multiple omics measurements are mapped to common reactions and pathways. However, data integration remains a challenge due to the complexity of the data and the difficulty in interpreting analysis results. RESULTS Here we present GraphOmics, a user-friendly platform to explore and integrate multiple omics datasets and support hypothesis generation. Users can upload transcriptomics, proteomics and metabolomics data to GraphOmics. Relevant entities are connected based on their biochemical relationships, and mapped to reactions and pathways from Reactome. From the Data Browser in GraphOmics, mapped entities and pathways can be ranked, sorted and filtered according to their statistical significance (p values) and fold changes. Context-sensitive panels provide information on the currently selected entities, while interactive heatmaps and clustering functionalities are also available. As a case study, we demonstrated how GraphOmics was used to interactively explore multi-omics data and support hypothesis generation using two complex datasets from existing Zebrafish regeneration and Covid-19 human studies. CONCLUSIONS GraphOmics is fully open-sourced and freely accessible from https://graphomics.glasgowcompbio.org/ . It can be used to integrate multiple omics data horizontally by mapping entities across omics to reactions and pathways. Our demonstration showed that by using interactive explorations from GraphOmics, interesting insights and biological hypotheses could be rapidly revealed.
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Affiliation(s)
- Joe Wandy
- Glasgow Polyomics, University of Glasgow, Glasgow, G61 1BD, UK
| | - Rónán Daly
- Glasgow Polyomics, University of Glasgow, Glasgow, G61 1BD, UK.
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11
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Katz L, Tata A, Woolman M, Zarrine-Afsar A. Lipid Profiling in Cancer Diagnosis with Hand-Held Ambient Mass Spectrometry Probes: Addressing the Late-Stage Performance Concerns. Metabolites 2021; 11:metabo11100660. [PMID: 34677375 PMCID: PMC8537725 DOI: 10.3390/metabo11100660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023] Open
Abstract
Untargeted lipid fingerprinting with hand-held ambient mass spectrometry (MS) probes without chromatographic separation has shown promise in the rapid characterization of cancers. As human cancers present significant molecular heterogeneities, careful molecular modeling and data validation strategies are required to minimize late-stage performance variations of these models across a large population. This review utilizes parallels from the pitfalls of conventional protein biomarkers in reaching bedside utility and provides recommendations for robust modeling as well as validation strategies that could enable the next logical steps in large scale assessment of the utility of ambient MS profiling for cancer diagnosis. Six recommendations are provided that range from careful initial determination of clinical added value to moving beyond just statistical associations to validate lipid involvements in disease processes mechanistically. Further guidelines for careful selection of suitable samples to capture expected and unexpected intragroup variance are provided and discussed in the context of demographic heterogeneities in the lipidome, further influenced by lifestyle factors, diet, and potential intersect with cancer lipid pathways probed in ambient mass spectrometry profiling studies.
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Affiliation(s)
- Lauren Katz
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy;
| | - Michael Woolman
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Arash Zarrine-Afsar
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
- Correspondence: ; Tel.: +1-416-581-8473
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12
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Maia M, Figueiredo A, Cordeiro C, Sousa Silva M. FT-ICR-MS-based metabolomics: A deep dive into plant metabolism. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34545595 DOI: 10.1002/mas.21731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics involves the identification and quantification of metabolites to unravel the chemical footprints behind cellular regulatory processes and to decipher metabolic networks, opening new insights to understand the correlation between genes and metabolites. In plants, it is estimated the existence of hundreds of thousands of metabolites and the majority is still unknown. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a powerful analytical technique to tackle such challenges. The resolving power and sensitivity of this ultrahigh mass accuracy mass analyzer is such that a complex mixture, such as plant extracts, can be analyzed and thousands of metabolite signals can be detected simultaneously and distinguished based on the naturally abundant elemental isotopes. In this review, FT-ICR-MS-based plant metabolomics studies are described, emphasizing FT-ICR-MS increasing applications in plant science through targeted and untargeted approaches, allowing for a better understanding of plant development, responses to biotic and abiotic stresses, and the discovery of new natural nutraceutical compounds. Improved metabolite extraction protocols compatible with FT-ICR-MS, metabolite analysis methods and metabolite identification platforms are also explored as well as new in silico approaches. Most recent advances in MS imaging are also discussed.
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Affiliation(s)
- Marisa Maia
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Lisboa, Portugal
| | - Andreia Figueiredo
- Departamento de Biologia Vegetal, Faculdade de Ciências, Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Lisboa, Portugal
| | - Carlos Cordeiro
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Marta Sousa Silva
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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13
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Safety assessment of cosmetics by read across applied to metabolomics data of in vitro skin and liver models. Arch Toxicol 2021; 95:3303-3322. [PMID: 34459931 DOI: 10.1007/s00204-021-03136-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
As a result of the cosmetics testing ban, safety evaluations of cosmetics ingredients must now be conducted using animal-free methods. A common approach is read across, which is mainly based on structural similarities but can also be conducted using biological endpoints. Here, metabolomics was used to assess biological effects to enable a read across between a candidate cosmetic ingredient, DIV665, only studied using in vitro assays, and a structurally similar reference compound, PA102, previously investigated using traditional in vivo toxicity methods. The (1) cutaneous distribution after topical application, (2) skin metabolism, (3) liver metabolism and (4) effect on the intracellular metabolomic profiles of in vitro skin and hepatic models, SkinEthic®RHE model and HepaRG® cells were investigated. The compounds exhibited similar skin penetration and skin and liver metabolism, with small differences attributed to their physicochemical properties. The effects of both compounds on the metabolome of RHE and HepaRG® cells were similarly small, both in terms of the metabolites modulated and the magnitude of changes. The patterns of metabolome changes did not fit with any known signature relating to a mode of action known to be linked to liver toxicity e.g. modification of the Krebs cycle, urea synthesis and lipid metabolism, were more reflective of transient adaptive responses. Overall, these studies indicate that PA102 is biologically similar to DIV665, allowing read across of safety endpoints, such as in vivo sub-chronic (but not reproduction toxicity) studies, for the former to be applied to DIV665. Based on this, in the absence of animal data (which is prohibited for new chemicals), it could be concluded that DIV665 applied according to the consumer topical use scenario, is similar to PA102, and is predicted to exhibit low local skin and systemic toxicity.
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14
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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15
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Boccard J, Schvartz D, Codesido S, Hanafi M, Gagnebin Y, Ponte B, Jourdan F, Rudaz S. Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model. Front Mol Biosci 2021; 8:682559. [PMID: 34055893 PMCID: PMC8163225 DOI: 10.3389/fmolb.2021.682559] [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: 03/18/2021] [Accepted: 04/19/2021] [Indexed: 01/21/2023] Open
Abstract
Because of its ability to generate biological hypotheses, metabolomics offers an innovative and promising approach in many fields, including clinical research. However, collecting specimens in this setting can be difficult to standardize, especially when groups of patients with different degrees of disease severity are considered. In addition, despite major technological advances, it remains challenging to measure all the compounds defining the metabolic network of a biological system. In this context, the characterization of samples based on several analytical setups is now recognized as an efficient strategy to improve the coverage of metabolic complexity. For this purpose, chemometrics proposes efficient methods to reduce the dimensionality of these complex datasets spread over several matrices, allowing the integration of different sources or structures of metabolic information. Bioinformatics databases and query tools designed to describe and explore metabolic network models offer extremely useful solutions for the contextualization of potential biomarker subsets, enabling mechanistic hypotheses to be considered rather than simple associations. In this study, network principal component analysis was used to investigate samples collected from three cohorts of patients including multiple stages of chronic kidney disease. Metabolic profiles were measured using a combination of four analytical setups involving different separation modes in liquid chromatography coupled to high resolution mass spectrometry. Based on the chemometric model, specific patterns of metabolites, such as N-acetyl amino acids, could be associated with the different subgroups of patients. Further investigation of the metabolic signatures carried out using genome-scale network modeling confirmed both tryptophan metabolism and nucleotide interconversion as relevant pathways potentially associated with disease severity. Metabolic modules composed of chemically adjacent or close compounds of biological relevance were further investigated using carbon transfer reaction paths. Overall, the proposed integrative data analysis strategy allowed deeper insights into the metabolic routes associated with different groups of patients to be gained. Because of their complementary role in the knowledge discovery process, the association of chemometrics and bioinformatics in a common workflow is therefore shown as an efficient methodology to gain meaningful insights in a clinical context.
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Affiliation(s)
- Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Domitille Schvartz
- Translational Biomarker Group, Department of Internal Medicine Specialties, University of Geneva, Geneva, Switzerland
| | - Santiago Codesido
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Mohamed Hanafi
- Unité Statistique, Sensométrie et Chimiométrie, Nantes, France
| | - Yoric Gagnebin
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Belén Ponte
- Service of Nephrology and Hypertension, Department of Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Fabien Jourdan
- Toxalim, Research Centre in Food Toxicology, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
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16
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Meurs J, Scurr DJ, Lourdusamy A, Storer LCD, Grundy RG, Alexander MR, Rahman R, Kim DH. Sequential Orbitrap Secondary Ion Mass Spectrometry and Liquid Extraction Surface Analysis-Tandem Mass Spectrometry-Based Metabolomics for Prediction of Brain Tumor Relapse from Sample-Limited Primary Tissue Archives. Anal Chem 2021; 93:6947-6954. [PMID: 33900724 DOI: 10.1021/acs.analchem.0c05087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present here a novel surface mass spectrometry strategy to perform untargeted metabolite profiling of formalin-fixed paraffin-embedded pediatric ependymoma archives. Sequential Orbitrap secondary ion mass spectrometry (3D OrbiSIMS) and liquid extraction surface analysis-tandem mass spectrometry (LESA-MS/MS) permitted the detection of 887 metabolites (163 chemical classes) from pediatric ependymoma tumor tissue microarrays (diameter: <1 mm; thickness: 4 μm). From these 163 classes, 60 classes were detected with both techniques, whilst LESA-MS/MS and 3D OrbiSIMS individually allowed the detection of another 83 and 20 unique metabolite classes, respectively. Through data fusion and multivariate analysis, we were able to identify key metabolites and corresponding pathways predictive of tumor relapse, which were retrospectively confirmed by gene expression analysis with publicly available data. Altogether, this sequential mass spectrometry strategy has shown to be a versatile tool to perform high-throughput metabolite profiling on sample-limited tissue archives.
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Affiliation(s)
- Joris Meurs
- Advanced Materials & Healthcare Technologies Division, School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - David J Scurr
- Children's Brain Tumor Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Coates Road, Nottingham NG7 2RD, U.K
| | - Anbarasu Lourdusamy
- Children's Brain Tumor Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Coates Road, Nottingham NG7 2RD, U.K
| | - Lisa C D Storer
- Children's Brain Tumor Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Coates Road, Nottingham NG7 2RD, U.K
| | - Richard G Grundy
- Children's Brain Tumor Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Coates Road, Nottingham NG7 2RD, U.K
| | - Morgan R Alexander
- Advanced Materials & Healthcare Technologies Division, School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Ruman Rahman
- Children's Brain Tumor Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Coates Road, Nottingham NG7 2RD, U.K
| | - Dong-Hyun Kim
- Advanced Materials & Healthcare Technologies Division, School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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17
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Jendoubi T. Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer. Metabolites 2021; 11:184. [PMID: 33801081 PMCID: PMC8003953 DOI: 10.3390/metabo11030184] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria-hypothesis, data types, strategies, study design and study focus- to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.
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Affiliation(s)
- Takoua Jendoubi
- Department of Statistical Science, University College London, London WC1E 6BT, UK
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18
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Corral-Jara KF, Cantini L, Poupin N, Ye T, Rigaudière JP, Vincent SDS, Pinel A, Morio B, Capel F. An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids. Nutrients 2020; 12:E3864. [PMID: 33348802 PMCID: PMC7765958 DOI: 10.3390/nu12123864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Insulin resistance decreases the ability of insulin to inhibit hepatic gluconeogenesis, a key step in the development of metabolic syndrome. Metabolic alterations, fat accumulation, and fibrosis in the liver are closely related and contribute to the progression of comorbidities, such as hypertension, type 2 diabetes, or cancer. Omega 3 (n-3) polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), were identified as potent positive regulators of insulin sensitivity in vitro and in animal models. In the current study, we explored the effects of a transgenerational supplementation with EPA in mice exposed to an obesogenic diet on the regulation of microRNAs (miRNAs) and gene expression in the liver using high-throughput techniques. We implemented a comprehensive molecular systems biology approach, combining statistical tools, such as MicroRNA Master Regulator Analysis pipeline and Boolean modeling to integrate these biochemical processes. We demonstrated that EPA mediated molecular adaptations, leading to the inhibition of miR-34a-5p, a negative regulator of Irs2 as a master regulatory event leading to the inhibition of gluconeogenesis by insulin during the fasting-feeding transition. Omics data integration provided greater biological insight and a better understanding of the relationships between biological variables. Such an approach may be useful for deriving innovative data-driven hypotheses and for the discovery of molecular-biochemical mechanistic links.
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Affiliation(s)
- Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Laura Cantini
- Computational Systems Biology Team, Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France;
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France;
| | - Tao Ye
- GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries/BP 10142/, 67404 Illkirch, France;
| | - Jean Paul Rigaudière
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Sarah De Saint Vincent
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Alexandre Pinel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Lyon 1, 69310 Pierre Bénite, France;
| | - Frédéric Capel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
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19
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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20
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Seneviratne CJ, Suriyanarayanan T, Widyarman AS, Lee LS, Lau M, Ching J, Delaney C, Ramage G. Multi-omics tools for studying microbial biofilms: current perspectives and future directions. Crit Rev Microbiol 2020; 46:759-778. [PMID: 33030973 DOI: 10.1080/1040841x.2020.1828817] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The advent of omics technologies has greatly improved our understanding of microbial biology, particularly in the last two decades. The field of microbial biofilms is, however, relatively new, consolidated in the 1980s. The morphogenic switching by microbes from planktonic to biofilm phenotype confers numerous survival advantages such as resistance to desiccation, antibiotics, biocides, ultraviolet radiation, and host immune responses, thereby complicating treatment strategies for pathogenic microorganisms. Hence, understanding the mechanisms governing the biofilm phenotype can result in efficient treatment strategies directed specifically against molecular markers mediating this process. The application of omics technologies for studying microbial biofilms is relatively less explored and holds great promise in furthering our understanding of biofilm biology. In this review, we provide an overview of the application of omics tools such as transcriptomics, proteomics, and metabolomics as well as multi-omics approaches for studying microbial biofilms in the current literature. We also highlight how the use of omics tools directed at various stages of the biological information flow, from genes to metabolites, can be integrated via multi-omics platforms to provide a holistic view of biofilm biology. Following this, we propose a future artificial intelligence-based multi-omics platform that can predict the pathways associated with different biofilm phenotypes.
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Affiliation(s)
- Chaminda J Seneviratne
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Tanujaa Suriyanarayanan
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Armelia Sari Widyarman
- Department of Microbiology, Faculty of Dentistry, Trisakti University, Grogol, West Jakarta, Indonesia
| | - Lye Siang Lee
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Matthew Lau
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore
| | - Jianhong Ching
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Christopher Delaney
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
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21
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Balcerczyk A, Damblon C, Elena-Herrmann B, Panthu B, Rautureau GJP. Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures. Int J Mol Sci 2020; 21:E6843. [PMID: 32961865 PMCID: PMC7554780 DOI: 10.3390/ijms21186843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Biological organisms are constantly exposed to an immense repertoire of molecules that cover environmental or food-derived molecules and drugs, triggering a continuous flow of stimuli-dependent adaptations. The diversity of these chemicals as well as their concentrations contribute to the multiplicity of induced effects, including activation, stimulation, or inhibition of physiological processes and toxicity. Metabolism, as the foremost phenotype and manifestation of life, has proven to be immensely sensitive and highly adaptive to chemical stimuli. Therefore, studying the effect of endo- or xenobiotics over cellular metabolism delivers valuable knowledge to apprehend potential cellular activity of individual molecules and evaluate their acute or chronic benefits and toxicity. The development of modern metabolomics technologies such as mass spectrometry or nuclear magnetic resonance spectroscopy now offers unprecedented solutions for the rapid and efficient determination of metabolic profiles of cells and more complex biological systems. Combined with the availability of well-established cell culture techniques, these analytical methods appear perfectly suited to determine the biological activity and estimate the positive and negative effects of chemicals in a variety of cell types and models, even at hardly detectable concentrations. Metabolic phenotypes can be estimated from studying intracellular metabolites at homeostasis in vivo, while in vitro cell cultures provide additional access to metabolites exchanged with growth media. This article discusses analytical solutions available for metabolic phenotyping of cell culture metabolism as well as the general metabolomics workflow suitable for testing the biological activity of molecular compounds. We emphasize how metabolic profiling of cell supernatants and intracellular extracts can deliver valuable and complementary insights for evaluating the effects of xenobiotics on cellular metabolism. We note that the concepts and methods discussed primarily for xenobiotics exposure are widely applicable to drug testing in general, including endobiotics that cover active metabolites, nutrients, peptides and proteins, cytokines, hormones, vitamins, etc.
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Affiliation(s)
- Aneta Balcerczyk
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland;
| | - Christian Damblon
- Unité de Recherche MolSys, Faculté des sciences, Université de Liège, 4000 Liège, Belgium;
| | | | - Baptiste Panthu
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Univ Lyon, Université Claude Bernard Lyon 1, 69921 Oullins CEDEX, France;
- Hospices Civils de Lyon, Faculté de Médecine, Hôpital Lyon Sud, 69921 Oullins CEDEX, France
| | - Gilles J. P. Rautureau
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (CRMN FRE 2034 CNRS, UCBL, ENS Lyon), Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
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22
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Sales G, Calura E, Romualdi C. metaGraphite-a new layer of pathway annotation to get metabolite networks. Bioinformatics 2020; 35:1258-1260. [PMID: 30184047 DOI: 10.1093/bioinformatics/bty719] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/17/2018] [Accepted: 09/03/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Metabolomics is an emerging 'omics' science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements. RESULTS We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks. AVAILABILITY AND IMPLEMENTATION The new graphite version (1.24) is available on Bioconductor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gabriele Sales
- Department of Biology, University of Padova, Padova, Italy
| | - Enrica Calura
- Department of Biology, University of Padova, Padova, Italy
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23
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Pezzatti J, Boccard J, Codesido S, Gagnebin Y, Joshi A, Picard D, González-Ruiz V, Rudaz S. Implementation of liquid chromatography-high resolution mass spectrometry methods for untargeted metabolomic analyses of biological samples: A tutorial. Anal Chim Acta 2020; 1105:28-44. [PMID: 32138924 DOI: 10.1016/j.aca.2019.12.062] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Abstract
Untargeted metabolomics is now widely recognized as a useful tool for exploring metabolic changes taking place in biological systems under different conditions. By its nature, this is a highly interdisciplinary field of research, and mastering all of the steps comprised in the pipeline can be a challenging task, especially for those researchers new to the topic. In this tutorial, we aim to provide an overview of the most widely adopted methods of performing LC-HRMS-based untargeted metabolomics of biological samples. A detailed protocol is provided in the Supplementary Information for rapidly implementing a basic screening workflow in a laboratory setting. This tutorial covers experimental design, sample preparation and analysis, signal processing and data treatment, and, finally, data analysis and its biological interpretation. Each section is accompanied by up-to-date literature to guide readers through the preparation and optimization of such a workflow, as well as practical information for avoiding or fixing some of the most frequently encountered pitfalls.
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Affiliation(s)
- Julian Pezzatti
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Julien Boccard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Santiago Codesido
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Yoric Gagnebin
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Abhinav Joshi
- Department of Cell Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Didier Picard
- Department of Cell Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland.
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24
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Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics. Methods Mol Biol 2020; 2064:191-217. [PMID: 31565776 DOI: 10.1007/978-1-4939-9831-9_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this age of -omics data-guided big data revolution, metabolomics has received significant attention as compared to genomics, transcriptomics, and proteomics for its proximity to the phenotype, the promises it makes and the challenges it throws. Although metabolomes of entire organisms, organs, biofluids, and tissues are of immense interest, a cell-specific resolution is deemed critical for biomedical applications where a granular understanding of cellular metabolism at cell-type and subcellular resolution is desirable. Mass spectrometry (MS) is a versatile technique that is used to analyze a broad range of compounds from different species and cell-types, with high accuracy, resolution, sensitivity, selectivity, and fast data acquisition speeds. With recent advances in MS and spectroscopy-based platforms, the research community is able to generate high-throughput data sets from single cells. However, it is challenging to handle, store, process, analyze, and interpret data in a routine manner. In this treatise, I present a workflow of metabolomics data generation from single cells and single-cell types to their analysis, visualization, and interpretation for obtaining biological insights.
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25
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Ivanisevic J, Want EJ. From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data. Metabolites 2019; 9:metabo9120308. [PMID: 31861212 PMCID: PMC6950334 DOI: 10.3390/metabo9120308] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
Untargeted metabolomics (including lipidomics) is a holistic approach to biomarker discovery and mechanistic insights into disease onset and progression, and response to intervention. Each step of the analytical and statistical pipeline is crucial for the generation of high-quality, robust data. Metabolite identification remains the bottleneck in these studies; therefore, confidence in the data produced is paramount in order to maximize the biological output. Here, we outline the key steps of the metabolomics workflow and provide details on important parameters and considerations. Studies should be designed carefully to ensure appropriate statistical power and adequate controls. Subsequent sample handling and preparation should avoid the introduction of bias, which can significantly affect downstream data interpretation. It is not possible to cover the entire metabolome with a single platform; therefore, the analytical platform should reflect the biological sample under investigation and the question(s) under consideration. The large, complex datasets produced need to be pre-processed in order to extract meaningful information. Finally, the most time-consuming steps are metabolite identification, as well as metabolic pathway and network analysis. Here we discuss some widely used tools and the pitfalls of each step of the workflow, with the ultimate aim of guiding the reader towards the most efficient pipeline for their metabolomics studies.
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Affiliation(s)
- Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 19, 1005 Lausanne, Switzerland
- Correspondence: (J.I.); (E.J.W.)
| | - Elizabeth J. Want
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
- Correspondence: (J.I.); (E.J.W.)
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26
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Razzaq A, Sadia B, Raza A, Khalid Hameed M, Saleem F. Metabolomics: A Way Forward for Crop Improvement. Metabolites 2019; 9:E303. [PMID: 31847393 PMCID: PMC6969922 DOI: 10.3390/metabo9120303] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Ali Raza
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China;
| | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
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27
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Rinschen MM, Palygin O, Guijas C, Palermo A, Palacio-Escat N, Domingo-Almenara X, Montenegro-Burke R, Saez-Rodriguez J, Staruschenko A, Siuzdak G. Metabolic rewiring of the hypertensive kidney. Sci Signal 2019; 12:12/611/eaax9760. [PMID: 31822592 DOI: 10.1126/scisignal.aax9760] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hypertension is a persistent epidemic across the developed world that is closely associated with kidney disease. Here, we applied a metabolomic, phosphoproteomic, and proteomic strategy to analyze the effect of hypertensive insults on kidneys. Our data revealed the metabolic aspects of hypertension-induced glomerular sclerosis, including lipid breakdown at early disease stages and activation of anaplerotic pathways to regenerate energy equivalents to counter stress. For example, branched-chain amino acids and proline, required for collagen synthesis, were depleted in glomeruli at early time points. Furthermore, indicators of metabolic stress were reflected by low amounts of ATP and NADH and an increased abundance of oxidized lipids derived from lipid breakdown. These processes were specific to kidney glomeruli where metabolic signaling occurred through mTOR and AMPK signaling. Quantitative phosphoproteomics combined with computational modeling suggested that these processes controlled key molecules in glomeruli and specifically podocytes, including cytoskeletal components and GTP-binding proteins, which would be expected to compete for decreasing amounts of GTP at early time points. As a result, glomeruli showed increased expression of metabolic enzymes of central carbon metabolism, amino acid degradation, and lipid oxidation, findings observed in previously published studies from other disease models and patients with glomerular damage. Overall, multilayered omics provides an overview of hypertensive kidney damage and suggests that metabolic or dietary interventions could prevent and treat glomerular disease and hypertension-induced nephropathy.
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Affiliation(s)
- Markus M Rinschen
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA.,Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne 50931, Germany
| | - Oleg Palygin
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Carlos Guijas
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Amelia Palermo
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Nicolas Palacio-Escat
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen 52074, Germany.,Institute of Computational Biomedicine, Bioquant, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg 69120, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg 69120, Germany
| | - Xavier Domingo-Almenara
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Rafael Montenegro-Burke
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Julio Saez-Rodriguez
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen 52074, Germany.,Institute of Computational Biomedicine, Bioquant, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg 69120, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and Heidelberg University, Heidelberg 69120, Germany
| | - Alexander Staruschenko
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA. .,Clement J. Zablocki VA Medical Center, Milwaukee, WI 53295, USA
| | - Gary Siuzdak
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA.
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28
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Frainay C, Aros S, Chazalviel M, Garcia T, Vinson F, Weiss N, Colsch B, Sedel F, Thabut D, Junot C, Jourdan F. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. Bioinformatics 2019; 35:274-283. [PMID: 29982278 PMCID: PMC6330003 DOI: 10.1093/bioinformatics/bty577] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Motivation Metabolomics has shown great potential to improve the understanding of complex diseases, potentially leading to therapeutic target identification. However, no single analytical method allows monitoring all metabolites in a sample, resulting in incomplete metabolic fingerprints. This incompleteness constitutes a stumbling block to interpretation, raising the need for methods that can enrich those fingerprints. We propose MetaboRank, a new solution inspired by social network recommendation systems for the identification of metabolites potentially related to a metabolic fingerprint. Results MetaboRank method had been used to enrich metabolomics data obtained on cerebrospinal fluid samples from patients suffering from hepatic encephalopathy (HE). MetaboRank successfully recommended metabolites not present in the original fingerprint. The quality of recommendations was evaluated by using literature automatic search, in order to check that recommended metabolites could be related to the disease. Complementary mass spectrometry experiments and raw data analysis were performed to confirm these suggestions. In particular, MetaboRank recommended the overlooked α-ketoglutaramate as a metabolite which should be added to the metabolic fingerprint of HE, thus suggesting that metabolic fingerprints enhancement can provide new insight on complex diseases. Availability and implementation Method is implemented in the MetExplore server and is available at www.metexplore.fr. A tutorial is available at https://metexplore.toulouse.inra.fr/com/tutorials/MetaboRank/2017-MetaboRank.pdf. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Clément Frainay
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | | | | | - Thomas Garcia
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Florence Vinson
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Nicolas Weiss
- Unité de Réanimation Neurologique, Département de Neurologie, Pôle des Maladies du Système Nerveux Central, Groupement Hospitalier Pitié-Salpêtrière Charles Foix, Assistance Publique - Hôpitaux de Paris, Paris, France.,Brain Liver Pitié-Salpêtrière (BLIPS) Study Group, Groupement Hospitalier Pitié-Salpêtrière-Charles Foix, Assistance Publique - Hôpitaux de Paris & INSERM UMR_S 938, CDR Saint-Antoine Maladies Métaboliques, Biliaires et Fibro-inflammatoire du Foie & Institut de Cardiométabolisme et Nutrition, ICAN, Paris, France
| | - Benoit Colsch
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, MetaboHUB, Gif-sur-Yvette, France and
| | | | - Dominique Thabut
- Brain Liver Pitié-Salpêtrière (BLIPS) Study Group, Groupement Hospitalier Pitié-Salpêtrière-Charles Foix, Assistance Publique - Hôpitaux de Paris & INSERM UMR_S 938, CDR Saint-Antoine Maladies Métaboliques, Biliaires et Fibro-inflammatoire du Foie & Institut de Cardiométabolisme et Nutrition, ICAN, Paris, France.,Unité de Soins Intensifs d'Hépato-gastroentérologie, Groupement Hospitalier Pitié-Salpêtrière-Charles Foix, Assistance Publique - Hôpitaux de Paris et Université Pierre et Marie Curie Paris 6, Paris, France
| | - Christophe Junot
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, MetaboHUB, Gif-sur-Yvette, France and
| | - Fabien Jourdan
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
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Megalios A, Daly R, Burgess K. MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics 2019; 34:2693-2694. [PMID: 29608638 PMCID: PMC6061834 DOI: 10.1093/bioinformatics/bty102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/27/2018] [Indexed: 12/02/2022] Open
Abstract
Motivation The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings. Results We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome. Availability and implementation https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/ Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anargyros Megalios
- Glasgow Polyomics, University of Glasgow, Glasgow, UK.,Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Karl Burgess
- Glasgow Polyomics, University of Glasgow, Glasgow, UK.,Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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30
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Cottret L, Frainay C, Chazalviel M, Cabanettes F, Gloaguen Y, Camenen E, Merlet B, Heux S, Portais JC, Poupin N, Vinson F, Jourdan F. MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Res 2019; 46:W495-W502. [PMID: 29718355 PMCID: PMC6030842 DOI: 10.1093/nar/gky301] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
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Affiliation(s)
- Ludovic Cottret
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Maxime Chazalviel
- INRA, UMR1331, Toxalim, F-31000 Toulouse, France.,MedDay Pharmaceuticals, Paris, France
| | | | - Yoann Gloaguen
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | | | - Stéphanie Heux
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France.,CNRS, UMR5504, F-31400 Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France.,CNRS, UMR5504, F-31400 Toulouse, France
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MetPC: Metabolite Pipeline Consisting of Metabolite Identification and Biomarker Discovery Under the Control of Two-Dimensional FDR. Metabolites 2019; 9:metabo9050103. [PMID: 31130635 PMCID: PMC6572057 DOI: 10.3390/metabo9050103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/12/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Due to the complex features of metabolomics data, the development of a unified platform, which covers preprocessing steps to data analysis, has been in high demand over the last few decades. Thus, we developed a new bioinformatics tool that includes a few of preprocessing steps and biomarker discovery procedure. For metabolite identification, we considered a hierarchical statistical model coupled with an Expectation–Maximization (EM) algorithm to take care of latent variables. For biomarker metabolite discovery, our procedure controls two-dimensional false discovery rate (fdr2d) when testing for multiple hypotheses simultaneously.
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32
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González-Peña D, Brennan L. Recent Advances in the Application of Metabolomics for Nutrition and Health. Annu Rev Food Sci Technol 2019; 10:479-519. [DOI: 10.1146/annurev-food-032818-121715] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolomics is the study of small molecules called metabolites in biological samples. Application of metabolomics to nutrition research has expanded in recent years, with emerging literature supporting multiple applications. Key examples include applications of metabolomics in the identification and development of objective biomarkers of dietary intake, in developing personalized nutrition strategies, and in large-scale epidemiology studies to understand the link between diet and health. In this review, we provide an overview of the current applications and identify key challenges that need to be addressed for the further development of the field. Successful development of metabolomics for nutrition research has the potential to improve dietary assessment, help deliver personalized nutrition, and enhance our understanding of the link between diet and health.
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Affiliation(s)
- Diana González-Peña
- School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin 4, Ireland;,
| | - Lorraine Brennan
- School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin 4, Ireland;,
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33
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Abstract
Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.
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34
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Rashmi D, Barvkar VT, Nadaf A, Mundhe S, Kadoo NY. Integrative omics analysis in Pandanus odorifer (Forssk.) Kuntze reveals the role of Asparagine synthetase in salinity tolerance. Sci Rep 2019; 9:932. [PMID: 30700750 PMCID: PMC6353967 DOI: 10.1038/s41598-018-37039-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/30/2018] [Indexed: 11/12/2022] Open
Abstract
Pandanus odorifer (Forssk) Kuntze grows naturally along the coastal regions and withstands salt-sprays as well as strong winds. A combination of omics approaches and enzyme activity studies was employed to comprehend the mechanistic basis of high salinity tolerance in P. odorifer. The young seedlings of P. odorifer were exposed to 1 M salt stress for up to three weeks and analyzed using RNAsequencing (RNAseq) and LC-MS. Integrative omics analysis revealed high expression of the Asparagine synthetase (AS) (EC 6.3.5.4) (8.95 fold) and remarkable levels of Asparagine (Asn) (28.5 fold). This indicated that salt stress promoted Asn accumulation in P. odorifer. To understand this further, the Asn biosynthesis pathway was traced out in P. odorifer. It was noticed that seven genes involved in Asn bisynthetic pathway namely glutamine synthetase (GS) (EC 6.3.1.2) glutamate synthase (GOGAT) (EC 1.4.1.14), aspartate kinase (EC 2.7.2.4), pyruvate kinase (EC 2.7.1.40), aspartate aminotransferase (AspAT) (EC 2.6.1.1), phosphoenolpyruvate carboxylase (PEPC) (EC 4.1.1.31) and AS were up-regulated under salt stress. AS transcripts were most abundant thereby showed its highest activity and thus were generating maximal Asn under salt stress. Also, an up-regulated Na+/H+ antiporter (NHX1) facilitated compartmentalization of Na+ into vacuoles, suggesting P. odorifer as salt accumulator species.
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Affiliation(s)
- Deo Rashmi
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Altafhusain Nadaf
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Swapnil Mundhe
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Narendra Y Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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35
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Sen P, Orešič M. Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. Metabolites 2019; 9:E22. [PMID: 30695998 PMCID: PMC6410263 DOI: 10.3390/metabo9020022] [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: 11/25/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/18/2022] Open
Abstract
There is growing interest in the metabolic interplay between the gut microbiome and host metabolism. Taxonomic and functional profiling of the gut microbiome by next-generation sequencing (NGS) has unveiled substantial richness and diversity. However, the mechanisms underlying interactions between diet, gut microbiome and host metabolism are still poorly understood. Genome-scale metabolic modeling (GSMM) is an emerging approach that has been increasingly applied to infer diet⁻microbiome, microbe⁻microbe and host⁻microbe interactions under physiological conditions. GSMM can, for example, be applied to estimate the metabolic capabilities of microbes in the gut. Here, we discuss how meta-omics datasets such as shotgun metagenomics, can be processed and integrated to develop large-scale, condition-specific, personalized microbiota models in healthy and disease states. Furthermore, we summarize various tools and resources available for metagenomic data processing and GSMM, highlighting the experimental approaches needed to validate the model predictions.
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Affiliation(s)
- Partho Sen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland.
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
| | - Matej Orešič
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland.
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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36
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Meshram RJ, Goundge MB, Kolte BS, Gacche RN. An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitol Int 2018; 69:59-70. [PMID: 30503238 DOI: 10.1016/j.parint.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022]
Abstract
Leishmaniasis is one of the major health issue in developing countries. The current therapeutic regimen for this disease is less effective with lot of adverse effects thereby warranting an urgent need to develop not only new and selective drug candidates but also identification of effective drug targets. Here we present subtractive genomics procedure for identification of putative drug targets in Leishmania. Comprehensive druggability analysis has been carried out in the current work for identified metabolic pathways and drug targets. We also demonstrate effective metabolic simulation methodology to pinpoint putative drug targets in threonine biosynthesis pathway. Metabolic simulation data from the current study indicate that decreasing flux through homoserine kinase reaction can be considered as a good therapeutic opportunity. The data from current study is expected to show new avenue for designing experimental strategies in search of anti-leishmanial agents.
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Affiliation(s)
- Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
| | - Mayuri B Goundge
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Baban S Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
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37
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Poupin N, Corlu A, Cabaton NJ, Dubois-Pot-Schneider H, Canlet C, Person E, Bruel S, Frainay C, Vinson F, Maurier F, Morel F, Robin MA, Fromenty B, Zalko D, Jourdan F. Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation. J Proteome Res 2018; 18:204-216. [PMID: 30394098 DOI: 10.1021/acs.jproteome.8b00524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Being able to explore the metabolism of broad metabolizing cells is of critical importance in many research fields. This article presents an original modeling solution combining metabolic network and omics data to identify modulated metabolic pathways and changes in metabolic functions occurring during differentiation of a human hepatic cell line (HepaRG). Our results confirm the activation of hepato-specific functionalities and newly evidence modulation of other metabolic pathways, which could not be evidenced from transcriptomic data alone. Our method takes advantage of the network structure to detect changes in metabolic pathways that do not have gene annotations and exploits flux analyses techniques to identify activated metabolic functions. Compared to the usual cell-specific metabolic network reconstruction approaches, it limits false predictions by considering several possible network configurations to represent one phenotype rather than one arbitrarily selected network. Our approach significantly enhances the comprehensive and functional assessment of cell metabolism, opening further perspectives to investigate metabolic shifts occurring within various biological contexts.
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Affiliation(s)
- Nathalie Poupin
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Anne Corlu
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Nicolas J Cabaton
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Hélène Dubois-Pot-Schneider
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Cécile Canlet
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Elodie Person
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Sandrine Bruel
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Clément Frainay
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Florence Vinson
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Florence Maurier
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Fabrice Morel
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Marie-Anne Robin
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Bernard Fromenty
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Daniel Zalko
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Fabien Jourdan
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
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38
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Gloaguen Y, Morton F, Daly R, Gurden R, Rogers S, Wandy J, Wilson D, Barrett M, Burgess K. PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data. Bioinformatics 2018; 33:4007-4009. [PMID: 28961954 PMCID: PMC5860087 DOI: 10.1093/bioinformatics/btx499] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/11/2017] [Indexed: 12/29/2022] Open
Abstract
Summary The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis from mass spectrometry data acquisition to biological interpretation. Our key innovations are the Summary Page, which provides a simple overview of the experiment in the format of a scientific paper, containing the key findings of the experiment along with associated metadata; and the Metabolite Page, which provides a list of each metabolite accompanied by ‘evidence cards’, which provide a variety of criteria behind metabolite annotation including peak shapes, intensities in different sample groups and database information. Availability and implementation PiMP is available at http://polyomics.mvls.gla.ac.uk, and access is freely available on request. 50 GB of space is allocated for data storage, with unrestricted number of samples and analyses per user. Source code is available at https://github.com/RonanDaly/pimp and licensed under the GPL. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoann Gloaguen
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics
| | - Fraser Morton
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics
| | - Ross Gurden
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics.,Centre for Cell Engineering
| | | | - Joe Wandy
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics.,School of Computing Science
| | - David Wilson
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics
| | - Michael Barrett
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics.,Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK
| | - Karl Burgess
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics
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39
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Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126. Arch Toxicol 2018; 92:2533-2547. [PMID: 29947894 PMCID: PMC6063328 DOI: 10.1007/s00204-018-2235-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022]
Abstract
Chemical pollutant exposure is a risk factor contributing to the growing epidemic of non-alcoholic fatty liver disease (NAFLD) affecting human populations that consume a western diet. Although it is recognized that intoxication by chemical pollutants can lead to NAFLD, there is limited information available regarding the mechanism by which typical environmental levels of exposure can contribute to the onset of this disease. Here, we describe the alterations in gene expression profiles and metabolite levels in the human HepaRG liver cell line, a validated model for cellular steatosis, exposed to the polychlorinated biphenyl (PCB) 126, one of the most potent chemical pollutants that can induce NAFLD. Sparse partial least squares classification of the molecular profiles revealed that exposure to PCB 126 provoked a decrease in polyunsaturated fatty acids as well as an increase in sphingolipid levels, concomitant with a decrease in the activity of genes involved in lipid metabolism. This was associated with an increased oxidative stress reflected by marked disturbances in taurine metabolism. A gene ontology analysis showed hallmarks of an activation of the AhR receptor by dioxin-like compounds. These changes in metabolome and transcriptome profiles were observed even at the lowest concentration (100 pM) of PCB 126 tested. A decrease in docosatrienoate levels was the most sensitive biomarker. Overall, our integrated multi-omics analysis provides mechanistic insight into how this class of chemical pollutant can cause NAFLD. Our study lays the foundation for the development of molecular signatures of toxic effects of chemicals causing fatty liver diseases to move away from a chemical risk assessment based on in vivo animal experiments.
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40
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Pujos-Guillot E, Brandolini-Bunlon M, Fouillet H, Joly C, Martin JF, Huneau JF, Dardevet D, Mariotti F. Metabolomics Reveals that the Type of Protein in a High-Fat Meal Modulates Postprandial Mitochondrial Overload and Incomplete Substrate Oxidation in Healthy Overweight Men. J Nutr 2018; 148:876-884. [PMID: 29878266 DOI: 10.1093/jn/nxy049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 01/30/2023] Open
Abstract
Background A meal rich in saturated fatty acids induces a postprandial metabolic challenge. The type of dietary protein may modulate postprandial metabolism. Objective We studied the effect of dietary protein type on postprandial changes in the metabolome after a high-fat meal. Methods In a 3-period, crossover, postprandial study, 10 healthy overweight men with an elevated waist circumference (>94 cm) ingested high-fat meals made up of cream fat (70% of energy), sucrose (15% energy), and protein (15% energy) from either casein (CAS), whey protein (WHE), or α-lactalbumin-enriched whey protein (LAC). Urine collected immediately before and 2, 4, and 6 h after the meal was analyzed for metabolomics, a secondary outcome of the clinical study. We used mixed-effect models, partial least-square regression, and pathway enrichment analysis. Results At 4 and 6 h after the meal, the postprandial metabolome was found to be fully discriminated according to protein type. We identified 17 metabolites that significantly explained the effect of protein type on postprandial metabolomic changes (protein-time interaction). Among this signature, acylcarnitines and other acylated metabolites related to fatty acid or amino acid oxidation were the main discriminant features. The difference in metabolic profiles was mainly explained by urinary acylcarnitines and some other acylated products (protein type, Ps < 0.0001), with a dramatically greater increase (100- to 1000-fold) after WHE, and to a lesser extent after LAC, as compared with CAS. Pathway enrichment analysis confirmed that the type of protein had modified fatty acid oxidation (P < 0.05). Conclusion Taken together, our results indicate that, in healthy overweight men, the type of protein in a high-fat meal interplays with fatty acid oxidation with a differential accumulation of incomplete oxidation products. A high-fat meal containing WHE, but not CAS, resulted in this outpacing of the tricarboxylic acid cycle. This study was registered at clinicaltrials.gov as NCT00931151.
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Affiliation(s)
- Estelle Pujos-Guillot
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, PFEM, MetaboHUB-Clermont, CRNH Auvergne, Clermont-Ferrand, France
| | - Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, PFEM, MetaboHUB-Clermont, CRNH Auvergne, Clermont-Ferrand, France
| | - Hélène Fouillet
- UMR PNCA, AgroParisTech, INRA, Université Paris-Saclay, 75005, Paris, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, PFEM, MetaboHUB-Clermont, CRNH Auvergne, Clermont-Ferrand, France
| | - Jean-François Martin
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, PFEM, MetaboHUB-Clermont, CRNH Auvergne, Clermont-Ferrand, France
| | | | - Dominique Dardevet
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - François Mariotti
- UMR PNCA, AgroParisTech, INRA, Université Paris-Saclay, 75005, Paris, France
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41
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Del Mar Amador M, Colsch B, Lamari F, Jardel C, Ichou F, Rastetter A, Sedel F, Jourdan F, Frainay C, Wevers RA, Roze E, Depienne C, Junot C, Mochel F. Targeted versus untargeted omics - the CAFSA story. J Inherit Metab Dis 2018; 41:447-456. [PMID: 29423831 DOI: 10.1007/s10545-017-0134-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/11/2017] [Accepted: 12/28/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND In 2009, untargeted metabolomics led to the delineation of a new clinico-biological entity called cerebellar ataxia with elevated cerebrospinal free sialic acid, or CAFSA. In order to elucidate CAFSA, we applied sequentially targeted and untargeted omic approaches. METHODS AND RESULTS First, we studied five of the six CAFSA patients initially described. Besides increased CSF free sialic acid concentrations, three patients presented with markedly decreased 5-methyltetrahydrofolate (5-MTHF) CSF concentrations. Exome sequencing identified a homozygous POLG mutation in two affected sisters, but failed to identify a causative gene in the three sporadic patients with high sialic acid but low 5-MTHF. Using targeted mass spectrometry, we confirmed that free sialic acid was increased in the CSF of a third known POLG-mutated patient. We then pursued pathophysiological analyses of CAFSA using mass spectrometry-based metabolomics on CSF from two sporadic CAFSA patients as well as 95 patients with an unexplained encephalopathy and 39 controls. This led to the identification of a common metabotype between the two initial CAFSA patients and three additional patients, including one patient with Kearns-Sayre syndrome. Metabolites of the CSF metabotype were positioned in a reconstruction of the human metabolic network, which highlighted the proximity of the metabotype with acetyl-CoA and carnitine, two key metabolites regulating mitochondrial energy homeostasis. CONCLUSION Our genetic and metabolomics analyses suggest that CAFSA is a heterogeneous entity related to mitochondrial DNA alterations either through POLG mutations or a mechanism similar to what is observed in Kearns-Sayre syndrome.
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Affiliation(s)
- Maria Del Mar Amador
- Assistance Publique-Hôpitaux de Paris, Département de Neurologie, La Pitié-Salpêtrière University Hospital, Paris, France
| | - Benoit Colsch
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Foudil Lamari
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Biochimie Métabolique, La Pitié-Salpêtrière University Hospital, Paris, France
- Université Pierre et Marie Curie, Groupe de Recherche Clinique Neurométabolique et Centre de Référence Neurométabolique Adulte, Paris, France
| | - Claude Jardel
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Biochimie Métabolique, La Pitié-Salpêtrière University Hospital, Paris, France
- Université Pierre et Marie Curie, Groupe de Recherche Clinique Neurométabolique et Centre de Référence Neurométabolique Adulte, Paris, France
| | - Farid Ichou
- Institute of Cardiometabolism And Nutrition, ICAN, Metabolomics Core Facility, Paris, France
| | - Agnès Rastetter
- Sorbonne Universités, UPMC-Paris 6, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, F-75013, Paris, France
| | | | - Fabien Jourdan
- Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Clément Frainay
- Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Ronald A Wevers
- Radboud University Medical Centre, Translational Metabolic Laboratory, Department Laboratory Medicine, Nijmegen, the Netherlands
| | - Emmanuel Roze
- Assistance Publique-Hôpitaux de Paris, Département de Neurologie, La Pitié-Salpêtrière University Hospital, Paris, France
- Université Pierre et Marie Curie, Groupe de Recherche Clinique Neurométabolique et Centre de Référence Neurométabolique Adulte, Paris, France
- Sorbonne Universités, UPMC-Paris 6, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, F-75013, Paris, France
| | - Christel Depienne
- Hôpitaux Universitaires de Strasbourg, Unité de cytogénétique chromosomique et moléculaire, Strasbourg, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Fanny Mochel
- Université Pierre et Marie Curie, Groupe de Recherche Clinique Neurométabolique et Centre de Référence Neurométabolique Adulte, Paris, France.
- Sorbonne Universités, UPMC-Paris 6, UMR S 1127, and Inserm U 1127, and CNRS UMR 7225, and ICM, F-75013, Paris, France.
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, La Pitié-Salpêtrière University Hospital, Paris, France.
- Reference Center for Neurometabolic Diseases, Department of Genetics, La Pitié-Salpêtrière University Hospital, 47 Boulevard de l'Hôpital, 75013, Paris, France.
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42
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The Rosa genome provides new insights into the domestication of modern roses. Nat Genet 2018; 50:772-777. [PMID: 29713014 PMCID: PMC5984618 DOI: 10.1038/s41588-018-0110-3] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/14/2018] [Indexed: 11/26/2022]
Abstract
Roses hold high cultural and economic importance as ornamentals and for the perfume industry. We report the rose whole genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern roses progenitor, Rosa chinensis ‘Old Blush’. Using Single Molecule Real-Time sequencing and a meta-assembly approach we obtained one of the most complete plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and recurrent blooming of Chinese species. Genomic segments of Chinese ancestry revealed new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and will accelerate improvement in roses, Rosaceae and ornamentals.
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Wang J, Wang C, Liu H, Qi H, Chen H, Wen J. Metabolomics assisted metabolic network modeling and network wide analysis of metabolites in microbiology. Crit Rev Biotechnol 2018; 38:1106-1120. [DOI: 10.1080/07388551.2018.1462141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Junhua Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People’s Republic of China
| | - Cheng Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People’s Republic of China
| | - Huanhuan Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, School of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Haishan Qi
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People’s Republic of China
| | - Hong Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People’s Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People’s Republic of China
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Rodriguez-Martinez A, Ayala R, Posma JM, Dumas ME. Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal. ACTA ACUST UNITED AC 2018; 61:14.14.1-14.14.13. [DOI: 10.1002/cpbi.41] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Andrea Rodriguez-Martinez
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, South Kensington Campus, Imperial College London; London United Kingdom
| | - Rafael Ayala
- Section of Structural Biology, Department of Medicine, Faculty of Medicine, South Kensington Campus, Imperial College London; London United Kingdom
| | - Joram M. Posma
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, South Kensington Campus, Imperial College London; London United Kingdom
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, South Kensington Campus, Imperial College London; London United Kingdom
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Forsberg EM, Huan T, Rinehart D, Benton HP, Warth B, Hilmers B, Siuzdak G. Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. Nat Protoc 2018; 13:633-651. [PMID: 29494574 PMCID: PMC5937130 DOI: 10.1038/nprot.2017.151] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to facilitating data interpretation in large-scale analyses. Global metabolomics is one such method for performing systems biology, as metabolites represent the downstream functional products of ongoing biological processes. We have developed XCMS Online, a platform that enables online metabolomics data processing and interpretation. A systems biology workflow recently implemented within XCMS Online enables rapid metabolic pathway mapping using raw metabolomics data for investigating dysregulated metabolic processes. In addition, this platform supports integration of multi-omic (such as genomic and proteomic) data to garner further systems-wide mechanistic insight. Here, we provide an in-depth procedure showing how to effectively navigate and use the systems biology workflow within XCMS Online without a priori knowledge of the platform, including uploading liquid chromatography (LC)-mass spectrometry (MS) data from metabolite-extracted biological samples, defining the job parameters to identify features, correcting for retention time deviations, conducting statistical analysis of features between sample classes and performing predictive metabolic pathway analysis. Additional multi-omics data can be uploaded and overlaid with previously identified pathways to enhance systems-wide analysis of the observed dysregulations. We also describe unique visualization tools to assist in elucidation of statistically significant dysregulated metabolic pathways. Parameter input takes 5-10 min, depending on user experience; data processing typically takes 1-3 h, and data analysis takes ∼30 min.
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Affiliation(s)
- Erica M Forsberg
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, USA
| | - Tao Huan
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
| | - Duane Rinehart
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
| | - H Paul Benton
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
| | - Benedikt Warth
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria
| | - Brian Hilmers
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
| | - Gary Siuzdak
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
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Shameer S, Baghalian K, Cheung CYM, Ratcliffe RG, Sweetlove LJ. Computational analysis of the productivity potential of CAM. NATURE PLANTS 2018; 4:165-171. [PMID: 29483685 DOI: 10.1038/s41477-018-0112-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/18/2018] [Indexed: 05/24/2023]
Abstract
There is considerable interest in transferring crassulacean acid metabolism (CAM) to C3 crops to improve their water-use efficiency. However, because the CAM biochemical cycle is energetically costly, it is unclear what impact this would have on yield. Using diel flux balance analysis of the CAM and C3 leaf metabolic networks, we show that energy consumption is three-fold higher in CAM at night. However, this additional cost of CAM can be entirely offset by the carbon-concentrating effect of malate decarboxylation behind closed stomata during the day. Depending on the resultant rates of the carboxylase and oxygenase activities of rubisco, the productivity of the PEPCK-CAM subtype is 74-100% of the C3 network. We conclude that CAM does not impose a significant productivity penalty and that engineering CAM into C3 crops is likely to lead to a major increase in water-use efficiency without substantially affecting yield.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford, UK.
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Rosato A, Tenori L, Cascante M, De Atauri Carulla PR, Martins Dos Santos VAP, Saccenti E. From correlation to causation: analysis of metabolomics data using systems biology approaches. Metabolomics 2018; 14:37. [PMID: 29503602 PMCID: PMC5829120 DOI: 10.1007/s11306-018-1335-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Metabolomics is a well-established tool in systems biology, especially in the top-down approach. Metabolomics experiments often results in discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, the interpretation of metabolomics data can be boosted by deploying systems biology approaches. OBJECTIVES This review aims to provide an overview of systems biology approaches that are relevant to metabolomics and to discuss some successful applications of these methods. METHODS We review the most recent applications of systems biology tools in the field of metabolomics, such as network inference and analysis, metabolic modelling and pathways analysis. RESULTS We offer an ample overview of systems biology tools that can be applied to address metabolomics problems. The characteristics and application results of these tools are discussed also in a comparative manner. CONCLUSIONS Systems biology-enhanced analysis of metabolomics data can provide insights into the molecular mechanisms originating the observed metabolic profiles and enhance the scientific impact of metabolomics studies.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Cascante
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Ramon De Atauri Carulla
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.
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Barupal DK, Fan S, Fiehn O. Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets. Curr Opin Biotechnol 2018; 54:1-9. [PMID: 29413745 DOI: 10.1016/j.copbio.2018.01.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 12/28/2022]
Abstract
Access to high quality metabolomics data has become a routine component for biological studies. However, interpreting those datasets in biological contexts remains a challenge, especially because many identified metabolites are not found in biochemical pathway databases. Starting from statistical analyses, a range of new tools are available, including metabolite set enrichment analysis, pathway and network visualization, pathway prediction, biochemical databases and text mining. Integrating these approaches into comprehensive and unbiased interpretations must carefully consider both caveats of the metabolomics dataset itself as well as the structure and properties of the biological study design. Special considerations need to be taken when adopting approaches from genomics for use in metabolomics. R and Python programming language are enabling an easier exchange of diverse tools to deploy integrated workflows. This review summarizes the key ideas and latest developments in regards to these approaches.
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Affiliation(s)
- Dinesh Kumar Barupal
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, United States
| | - Sili Fan
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, United States
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, United States; Biochemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
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Rodriguez-Martinez A, Ayala R, Posma JM, Neves AL, Gauguier D, Nicholson JK, Dumas ME. MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways. Bioinformatics 2018; 33:773-775. [PMID: 28011775 PMCID: PMC5408820 DOI: 10.1093/bioinformatics/btw697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/03/2016] [Indexed: 12/31/2022] Open
Abstract
Summary MetaboSignal is an R package that allows merging metabolic and signaling pathways reported in the Kyoto Encyclopaedia of Genes and Genomes (KEGG). It is a network-based approach designed to navigate through topological relationships between genes (signaling- or metabolic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape of metabolic phenotypes. Availability and Implementation MetaboSignal is available from Bioconductor: https://bioconductor.org/packages/MetaboSignal/ Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrea Rodriguez-Martinez
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
| | - Rafael Ayala
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
| | - Joram M Posma
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
| | - Ana L Neves
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
| | - Dominique Gauguier
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK.,Sorbonne Universities, University Pierre & Marie Curie, University Paris Descartes, Sorbonne Paris Cité, INSERMUMR_S 1138, Cordeliers Research Centre, 75006 Paris, France
| | - Jeremy K Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
| | - Marc-Emmanuel Dumas
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
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Marco-Ramell A, Palau-Rodriguez M, Alay A, Tulipani S, Urpi-Sarda M, Sanchez-Pla A, Andres-Lacueva C. Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. BMC Bioinformatics 2018; 19:1. [PMID: 29291722 PMCID: PMC5749025 DOI: 10.1186/s12859-017-2006-0] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/18/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Bioinformatic tools for the enrichment of 'omics' datasets facilitate interpretation and understanding of data. To date few are suitable for metabolomics datasets. The main objective of this work is to give a critical overview, for the first time, of the performance of these tools. To that aim, datasets from metabolomic repositories were selected and enriched data were created. Both types of data were analysed with these tools and outputs were thoroughly examined. RESULTS An exploratory multivariate analysis of the most used tools for the enrichment of metabolite sets, based on a non-metric multidimensional scaling (NMDS) of Jaccard's distances, was performed and mirrored their diversity. Codes (identifiers) of the metabolites of the datasets were searched in different metabolite databases (HMDB, KEGG, PubChem, ChEBI, BioCyc/HumanCyc, LipidMAPS, ChemSpider, METLIN and Recon2). The databases that presented more identifiers of the metabolites of the dataset were PubChem, followed by METLIN and ChEBI. However, these databases had duplicated entries and might present false positives. The performance of over-representation analysis (ORA) tools, including BioCyc/HumanCyc, ConsensusPathDB, IMPaLA, MBRole, MetaboAnalyst, Metabox, MetExplore, MPEA, PathVisio and Reactome and the mapping tool KEGGREST, was examined. Results were mostly consistent among tools and between real and enriched data despite the variability of the tools. Nevertheless, a few controversial results such as differences in the total number of metabolites were also found. Disease-based enrichment analyses were also assessed, but they were not found to be accurate probably due to the fact that metabolite disease sets are not up-to-date and the difficulty of predicting diseases from a list of metabolites. CONCLUSIONS We have extensively reviewed the state-of-the-art of the available range of tools for metabolomic datasets, the completeness of metabolite databases, the performance of ORA methods and disease-based analyses. Despite the variability of the tools, they provided consistent results independent of their analytic approach. However, more work on the completeness of metabolite and pathway databases is required, which strongly affects the accuracy of enrichment analyses. Improvements will be translated into more accurate and global insights of the metabolome.
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Affiliation(s)
- Anna Marco-Ramell
- Biomarkers & Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Food Technology Reference Net (XaRTA), Nutrition and Food Safety Research Institute (INSA-UB), Faculty of Pharmacy and Food Sciences, Pharmacy and Food Science Faculty, University of Barcelona, Barcelona, Spain
- CIBER Fragilidad y Envejecimiento Saludable [CIBERfes], Instituto de Salud Carlos III [ISCIII], Madrid, Spain
| | - Magali Palau-Rodriguez
- Biomarkers & Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Food Technology Reference Net (XaRTA), Nutrition and Food Safety Research Institute (INSA-UB), Faculty of Pharmacy and Food Sciences, Pharmacy and Food Science Faculty, University of Barcelona, Barcelona, Spain
- CIBER Fragilidad y Envejecimiento Saludable [CIBERfes], Instituto de Salud Carlos III [ISCIII], Madrid, Spain
| | - Ania Alay
- Genetics, Microbiology and Statistics Department, Biology Faculty, University of Barcelona, Barcelona, Spain
| | - Sara Tulipani
- Biomarkers & Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Food Technology Reference Net (XaRTA), Nutrition and Food Safety Research Institute (INSA-UB), Faculty of Pharmacy and Food Sciences, Pharmacy and Food Science Faculty, University of Barcelona, Barcelona, Spain
| | - Mireia Urpi-Sarda
- Biomarkers & Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Food Technology Reference Net (XaRTA), Nutrition and Food Safety Research Institute (INSA-UB), Faculty of Pharmacy and Food Sciences, Pharmacy and Food Science Faculty, University of Barcelona, Barcelona, Spain
- CIBER Fragilidad y Envejecimiento Saludable [CIBERfes], Instituto de Salud Carlos III [ISCIII], Madrid, Spain
| | - Alex Sanchez-Pla
- Genetics, Microbiology and Statistics Department, Biology Faculty, University of Barcelona, Barcelona, Spain
- Statistics and Bioinformatics Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Cristina Andres-Lacueva
- Biomarkers & Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Food Technology Reference Net (XaRTA), Nutrition and Food Safety Research Institute (INSA-UB), Faculty of Pharmacy and Food Sciences, Pharmacy and Food Science Faculty, University of Barcelona, Barcelona, Spain
- CIBER Fragilidad y Envejecimiento Saludable [CIBERfes], Instituto de Salud Carlos III [ISCIII], Madrid, Spain
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