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Tojo H, Tabeta H, Gunji S, Hirai MY, David P, Javot H, Ferjani A. Roles of type II H +-PPases and PPsPase1/PECP2 in early developmental stages and PPi homeostasis of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1031426. [PMID: 36778688 PMCID: PMC9911876 DOI: 10.3389/fpls.2023.1031426] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The regulation of intracellular pyrophosphate (PPi) level is crucial for proper morphogenesis across all taxonomic kingdoms. PPi is released as a byproduct from ~200 metabolic reactions, then hydrolyzed by either membrane-bound (H+-PPase) or soluble pyrophosphatases (PPases). In Arabidopsis, the loss of the vacuolar H+-PPase/FUGU5, a key enzyme in PPi homeostasis, results in delayed growth and a number of developmental defects, pointing to the importance of PPi homeostasis in plant morphogenesis. The Arabidopsis genome encodes several PPases in addition to FUGU5, such as PPsPase1/PECP2, VHP2;1 and VHP2;2, although their significance regarding PPi homeostasis remains elusive. Here, to assess their contribution, phenotypic analyses of cotyledon aspect ratio, palisade tissue cellular phenotypes, adaxial side pavement cell complexity, stomatal distribution, and etiolated seedling length were performed, provided that they were altered due to excess PPi in a fugu5 mutant background. Overall, our analyses revealed that the above five traits were unaffected in ppspase1/pecp2, vhp2;1 and vhp2;2 loss-of-function mutants, as well as in fugu5 mutant lines constitutively overexpressing PPsPase1/PECP2. Furthermore, metabolomics revealed that ppspase1/pecp2, vhp2;1 and vhp2;2 etiolated seedlings exhibited metabolic profiles comparable to the wild type. Together, these results indicate that the contribution of PPsPase1/PECP2, VHP2;1 and VHP2;2 to PPi levels is negligible in comparison to FUGU5 in the early stages of seedling development.
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Affiliation(s)
- Hiroshi Tojo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Hiromitsu Tabeta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Masami Y. Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Pascale David
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Hélène Javot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
- Aix Marseille Univ, CEA, CNRS, BIAM, Marseille, France
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
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2
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Tabeta H, Higashi Y, Okazaki Y, Toyooka K, Wakazaki M, Sato M, Saito K, Hirai MY, Ferjani A. Skotomorphogenesis exploits threonine to promote hypocotyl elongation. QUANTITATIVE PLANT BIOLOGY 2022; 3:e26. [PMID: 37077988 PMCID: PMC10095960 DOI: 10.1017/qpb.2022.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 05/02/2023]
Abstract
Mobilisation of seed storage reserves is important for seedling establishment in Arabidopsis. In this process, sucrose is synthesised from triacylglycerol via core metabolic processes. Mutants with defects in triacylglycerol-to-sucrose conversion display short etiolated seedlings. We found that whereas sucrose content in the indole-3-butyric acid response 10 (ibr10) mutant was significantly reduced, hypocotyl elongation in the dark was unaffected, questioning the role of IBR10 in this process. To dissect the metabolic complexity behind cell elongation, a quantitative-based phenotypic analysis combined with a multi-platform metabolomics approach was applied. We revealed that triacylglycerol and diacylglycerol breakdown were disrupted in ibr10, resulting in low sugar content and poor photosynthetic ability. Importantly, batch-learning self-organised map clustering revealed that threonine level was correlated with hypocotyl length. Consistently, exogenous threonine supply stimulated hypocotyl elongation, indicating that sucrose levels are not always correlated with etiolated seedling length, suggesting the contribution of amino acids in this process.
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Affiliation(s)
- Hiromitsu Tabeta
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | | | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masami Y Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
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3
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TRACES: A Lightweight Browser for Liquid Chromatography-Multiple Reaction Monitoring-Mass Spectrometry Chromatograms. Metabolites 2022; 12:metabo12040354. [PMID: 35448541 PMCID: PMC9027295 DOI: 10.3390/metabo12040354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022] Open
Abstract
In targeted metabolomic analysis using liquid chromatography–multiple reaction monitoring–mass spectrometry (LC-MRM-MS), hundreds of MRMs are performed in a single run, yielding a large dataset containing thousands of chromatographic peaks. Automation tools for processing large MRM datasets have been reported, but a visual review of chromatograms is still critical, as real samples with biological matrices often cause complex chromatographic patterns owing to non-specific, insufficiently separated, isomeric, and isotopic components. Herein, we report the development of new software, TRACES, a lightweight chromatogram browser for MRM-based targeted LC-MS analysis. TRACES provides rapid access to all MRM chromatograms in a dataset, allowing users to start ad hoc data browsing without preparations such as loading compound libraries. As a special function of the software, we implemented a chromatogram-level deisotoping function that facilitates the identification of regions potentially affected by isotopic signals. Using MRM libraries containing precursor and product formulae, the algorithm reveals all possible isotopic interferences in the dataset and generates deisotoped chromatograms. To validate the deisotoping function in real applications, we analyzed mouse tissue phospholipids in which isotopic interference by molecules with different fatty-acyl unsaturation levels is known. TRACES successfully removed isotopic signals within the MRM chromatograms, helping users avoid inappropriate regions for integration.
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4
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Dissecting the Mechanism of Action of Spiperone-A Candidate for Drug Repurposing for Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14030776. [PMID: 35159043 PMCID: PMC8834219 DOI: 10.3390/cancers14030776] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Despite advances in primary and adjuvant treatments, approximately 50% of colorectal cancer (CRC) patients still die from recurrence and metastatic disease. Thus, alternative and more effective therapeutic approaches are expected to be developed. Drug repurposing is increasing interest in cancer therapy, as it represents a cheaper and faster alternative strategy to de novo drug synthesis. Psychiatric medications are promising as a new generation of antitumor drugs. Here, we demonstrate that spiperone—a licensed drug for the treatment of schizophrenia—induces apoptosis in CRC cells. Our data reveal that spiperone’s cytotoxicity in CRC cells is mediated by phospholipase C activation, intracellular calcium homeostasis dysregulation, and irreversible endoplasmic reticulum stress induction, resulting in lipid metabolism alteration and Golgi apparatus damage. By identifying new targetable pathways in CRC cells, our findings represent a promising starting point for the design of novel therapeutic strategies for CRC. Abstract Approximately 50% of colorectal cancer (CRC) patients still die from recurrence and metastatic disease, highlighting the need for novel therapeutic strategies. Drug repurposing is attracting increasing attention because, compared to traditional de novo drug discovery processes, it may reduce drug development periods and costs. Epidemiological and preclinical evidence support the antitumor activity of antipsychotic drugs. Herein, we dissect the mechanism of action of the typical antipsychotic spiperone in CRC. Spiperone can reduce the clonogenic potential of stem-like CRC cells (CRC-SCs) and induce cell cycle arrest and apoptosis, in both differentiated and CRC-SCs, at clinically relevant concentrations whose toxicity is negligible for non-neoplastic cells. Analysis of intracellular Ca2+ kinetics upon spiperone treatment revealed a massive phospholipase C (PLC)-dependent endoplasmic reticulum (ER) Ca2+ release, resulting in ER Ca2+ homeostasis disruption. RNA sequencing revealed unfolded protein response (UPR) activation, ER stress, and induction of apoptosis, along with IRE1-dependent decay of mRNA (RIDD) activation. Lipidomic analysis showed a significant alteration of lipid profile and, in particular, of sphingolipids. Damage to the Golgi apparatus was also observed. Our data suggest that spiperone can represent an effective drug in the treatment of CRC, and that ER stress induction, along with lipid metabolism alteration, represents effective druggable pathways in CRC.
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An JN, Kim H, Kim EN, Cho A, Cho Y, Choi YW, Kim JH, Yang SH, Choi BS, Lim CS, Kim YS, Kim KP, Lee JP. Effects of periostin deficiency on kidney aging and lipid metabolism. Aging (Albany NY) 2021; 13:22649-22665. [PMID: 34607314 PMCID: PMC8544301 DOI: 10.18632/aging.203580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022]
Abstract
Periostin plays a crucial role in fibrosis, which is involved in kidney aging. A few studies have shown that lipid metabolism is involved in kidney aging. We investigated the role of periostin in lipid metabolism during kidney aging. Renal function, fibrosis, and inflammatory markers were studied using urine, blood, and tissue samples from wild-type (WT) C57BL/6 mice and Postn-null mice of 2 and 24 months of age. Lipids were quantitatively profiled using liquid chromatography-tandem mass spectrometry in the multiple reaction monitoring mode. Renal function was worse and tubular atrophy/interstitial fibrosis, periostin expression, and inflammatory and fibrotic markers were more severe in aged WT mice than in young WT mice. In aged Postn-null mice, these changes were mitigated. Thirty-five differentially regulated lipids were identified. Phosphatidylcholines, cholesteryl ester, cholesterol, ceramide-1-phosphate, and CCL5 expression were significantly higher in aged WT mice than in aged Postn-null mice. Particularly, linoleic acid, linolenic acid, arachidonic acid, and docosahexaenoic acid differed strongly between the two groups. Lysophosphatidylcholine acyltransferase 2, which converts lysophosphatidylcholine to phosphatidylcholine, was significantly higher in aged WT mice than in aged Postn-null mice. Periostin expression in the kidneys increased with age, and periostin ablation delayed aging. Changes in lipids and their metabolism were found in Postn-null mice. Further research on the precise mechanisms of and relationships between lipid expression and metabolism, kidney aging, and periostin expression is warranted.
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Affiliation(s)
- Jung Nam An
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Gyeonggi-do, Korea
| | - Hyoseon Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Korea
| | - Eun Nim Kim
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ara Cho
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Yeongeun Cho
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Korea
| | - Young Wook Choi
- Department of Urology, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Jin Hyuk Kim
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Seung Hee Yang
- Seoul National University Kidney Research Institute, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Bum Soon Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Chun Soo Lim
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Yon Su Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Korea
| | - Jung Pyo Lee
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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6
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Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D. SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. Anal Chem 2020; 92:15968-15974. [PMID: 33269929 DOI: 10.1021/acs.analchem.0c03421] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Technological advances in high-resolution mass spectrometry (MS) vastly increased the number of samples that can be processed in a life science experiment, as well as volume and complexity of the generated data. To address the bottleneck of high-throughput data processing, we present SmartPeak (https://github.com/AutoFlowResearch/SmartPeak), an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of capillary electrophoresis-, gas chromatography-, and liquid chromatography (LC)-MS(/MS) data and high-pressure LC data for targeted and semitargeted metabolomics, lipidomics, and fluxomics experiments. The application allows for an approximate 100-fold reduction in the data processing time compared to manual processing while enhancing quality and reproducibility of the results.
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Affiliation(s)
- Svetlana Kutuzova
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Pasquale Colaianni
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Hannes Röst
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto M5S 1A8, Canada.,Department of Computer Science, University of Toronto, 40 St. George Street, Toronto M5T 3A1, Canada
| | - Timo Sachsenberg
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72074, Germany
| | - Oliver Alka
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72074, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72074, Germany.,Biomolecular Interactions, MPI for Developmental Biology, Tübingen 72076, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen 72076, Germany
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 117456, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 117597, Singapore
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Mette Kristensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Lars Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark.,BioInnovation Institute, Ole Maaløes Vej 3, Copenhagen N 2830, Denmark
| | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
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7
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Yamamoto T, Takabatake Y, Minami S, Sakai S, Fujimura R, Takahashi A, Namba-Hamano T, Matsuda J, Kimura T, Matsui I, Kaimori JY, Takeda H, Takahashi M, Izumi Y, Bamba T, Matsusaka T, Niimura F, Yanagita M, Isaka Y. Eicosapentaenoic acid attenuates renal lipotoxicity by restoring autophagic flux. Autophagy 2020; 17:1700-1713. [PMID: 32546086 DOI: 10.1080/15548627.2020.1782034] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recently, we identified a novel mechanism of lipotoxicity in the kidney proximal tubular cells (PTECs); lipid overload stimulates macroautophagy/autophagy for the renovation of plasma and organelle membranes to maintain the integrity of the PTECs. However, this autophagic activation places a burden on the lysosomal system, leading to a downstream suppression of autophagy, which manifests as phospholipid accumulation and inadequate acidification in lysosomes. Here, we investigated whether pharmacological correction by eicosapentaenoic acid (EPA) supplementation could restore autophagic flux and alleviate renal lipotoxicity. EPA supplementation to high-fat diet (HFD)-fed mice reduced several hallmarks of lipotoxicity in the PTECs, such as phospholipid accumulation in the lysosome, mitochondrial dysfunction, inflammation, and fibrosis. In addition to improving the metabolic syndrome, EPA alleviated renal lipotoxicity via several mechanisms. EPA supplementation to HFD-fed mice or the isolated PTECs cultured in palmitic acid (PA) restored lysosomal function with significant improvements in the autophagic flux. The PA-induced redistribution of phospholipids from cellular membranes into lysosomes and the HFD-induced accumulation of SQSTM1/p62 (sequestosome 1), an autophagy substrate, during the temporal and genetic ablation of autophagy were significantly reduced by EPA, indicating that EPA attenuated the HFD-mediated increases in autophagy demand. Moreover, a fatty acid pulse-chase assay revealed that EPA promoted lipid droplet (LD) formation and transfer from LDs to the mitochondria for beta-oxidation. Noteworthy, the efficacy of EPA on lipotoxicity is autophagy-dependent and cell-intrinsic. In conclusion, EPA counteracts lipotoxicity in the proximal tubule by alleviating autophagic numbness, making it potentially suitable as a novel treatment for obesity-related kidney diseases.Abbreviations: 4-HNE: 4-hydroxy-2-nonenal; ACTB: actin beta; ADGRE1/F4/80: adhesion G protein-coupled receptor E1; ATG: autophagy-related; ATP: adenosine triphosphate; BODIPY: boron-dipyrromethene; BSA: bovine serum albumin; cKO: conditional knockout; CML: N-carboxymethyllysine; COL1A1: collagen type I alpha 1 chain; COX: cytochrome c oxidase; CTRL: control; DGAT: diacylglycerol O-acyltransferase; EPA: eicosapentaenoic acid; FA: fatty acid; FFA: free fatty acid; GFP: green fluorescent protein; HFD: high-fat diet; iKO: inducible knockout; IRI: ischemia-reperfusion injury; LAMP1: lysosomal-associated membrane protein 1; LD: lipid droplet; LRP2: low density lipoprotein receptor-related protein 2; MAP1LC3: microtubule-associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; OA: oleic acid; PAS: periodic-acid Schiff; PPAR: peroxisome proliferator activated receptor; PPARGC1/PGC1: peroxisome proliferator activated receptor, gamma, coactivator 1; PTEC: proximal tubular epithelial cell; ROS: reactive oxygen species; RPS6: ribosomal protein S6; SDH: succinate dehydrogenase complex; SFC/MS/MS: supercritical fluid chromatography triple quadrupole mass spectrometry; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB; TG: triglyceride; TUNEL: terminal deoxynucleotidyl transferase dUTP nick end labeling.
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Affiliation(s)
- Takeshi Yamamoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitsugu Takabatake
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Satoshi Minami
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinsuke Sakai
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ryuta Fujimura
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Takahashi
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomoko Namba-Hamano
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun Matsuda
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomonori Kimura
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan.,Reverse Translational Project, Center for Rare Disease Research, National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan.,KAGAMI Project, National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Isao Matsui
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun-Ya Kaimori
- Department of Advanced Technology for Transplantation, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroaki Takeda
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Taiji Matsusaka
- Institute of Medical Sciences and Department of Molecular Life Sciences, Tokai University School of Medicine, Kanagawa, Japan
| | - Fumio Niimura
- Department of Pediatrics, Tokai University School of Medicine, Kanagawa, Japan
| | - Motoko Yanagita
- Department of Nephrology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
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8
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Mohamed A, Molendijk J, Hill MM. lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets. J Proteome Res 2020; 19:2890-2897. [PMID: 32168452 DOI: 10.1021/acs.jproteome.0c00082] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rapid evolution of mass spectrometry (MS)-based lipidomics has enabled the simultaneous measurement of numerous lipid classes. With lipidomics datasets becoming increasingly available, lipidomic-focused software tools are required to facilitate data analysis as well as mining of public datasets, integrating lipidomics-unique molecular information such as lipid class, chain length, and unsaturation. To address this need, we developed lipidr, an open-source R/Bioconductor package for data mining and analysis of lipidomics datasets. lipidr implements a comprehensive lipidomic-focused analysis workflow for targeted and untargeted lipidomics. lipidr imports numerical matrices, Skyline exports, and Metabolomics Workbench files directly into R, automatically inferring lipid class and chain information from lipid names. Through integration with the Metabolomics Workbench API, users can search, download, and reanalyze public lipidomics datasets seamlessly. lipidr allows thorough data inspection, normalization, and uni- and multivariate analyses, displaying results as interactive visualizations. To enable interpretation of lipid class, chain length, and total unsaturation data, we also developed and implemented a novel lipid set enrichment analysis. A companion online guide with two live example datasets is presented at https://www.lipidr.org/. We expect that the ease of use and innovative features of lipidr will allow the lipidomics research community to gain novel detailed insights from lipidomics data.
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Affiliation(s)
- Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Jeffrey Molendijk
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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9
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Song L, Yin Q, Kang M, Ma N, Li X, Yang Z, Jin H, Lin M, Zhuang P, Zhang Y. Untargeted metabolomics reveals novel serum biomarker of renal damage in rheumatoid arthritis. J Pharm Biomed Anal 2019; 180:113068. [PMID: 31884392 DOI: 10.1016/j.jpba.2019.113068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 12/07/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic progressive disease, it often involves kidney, lung, heart, and other systems.Renal damage is quite common in RA. Exploring of biomarkers of renal damage in the course of RA progression is of significant importance for disease diagnosis and treatment. We use type II Collagen-Induced Arthritis(CIA) Model. Serums were collected at the 4th, 6th, 8th, and 10th week after the first immunization. An untargeted metabonomic strategy based on UPLC-Q/TOF/MS with support vector machine(SVM) was developed to discover the biomarkers in the rats' serum samples between the RA stage(4-6 weeks in RA model, at which time the kidneys are not affected) and renal damage in RA stage(8-10 weeks in RA model, and the kidneys are affected). Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) were used to analyze the metabolic profiles of rat serum. The support vector machine (SVM) method was used to screen the specific markers of renal damage in RA. Following multivariate statistical and integration analysis, 5 specific markers of renal damage in RA were screened and found. After the analysis of these metabolites, pentose and glucuronate interconversions are closely related to the pathogenesis of RA renal damage. The present study first use untargeted dmetabonomics combined with the pathological features in the different phases of CIA model rats. This will provide a basis for the choice of treatment drugs for patients with RA who may be complicated by renal damage.
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Affiliation(s)
- Lili Song
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Qingsheng Yin
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Mingqin Kang
- Jilin Entry-exit Inspection and Quarantine Bureau, Changchun, People's Republic of China
| | - Ningning Ma
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Xin Li
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Zhen Yang
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Hua Jin
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Mengya Lin
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China
| | - Pengwei Zhuang
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China.
| | - Yanjun Zhang
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Jian Kang Chan Ye Yuan, Jinghai Dist., Tianjin 301617, People's Republic of China.
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10
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Nyamugenda E, Trentzsch M, Russell S, Miles T, Boysen G, Phelan KD, Baldini G. Injury to hypothalamic Sim1 neurons is a common feature of obesity by exposure to high-fat diet in male and female mice. J Neurochem 2019; 149:73-97. [PMID: 30615192 DOI: 10.1111/jnc.14662] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/16/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
The hypothalamus is essential for regulation of energy homeostasis and metabolism. Feeding hypercaloric, high-fat (HF) diet induces hypothalamic arcuate nucleus injury and alters metabolism more severely in male than in female mice. The site(s) and extent of hypothalamic injury in male and female mice are not completely understood. In the paraventricular nucleus (PVN) of the hypothalamus, single-minded family basic helix-loop helix transcription factor 1 (Sim1) neurons are essential to control energy homeostasis. We tested the hypothesis that exposure to HF diet induces injury to Sim1 neurons in the PVN of male and female mice. Mice expressing membrane-bound enhanced green fluorescent protein (mEGFP) in Sim1 neurons (Sim1-Cre:Rosa-mEGFP mice) were generated to visualize the effects of exposure to HF diet on these neurons. Male and female Sim1-Cre:Rosa-mEGFP mice exposed to HF diet had increased weight, hyperleptinemia, and developed hepatosteatosis. In male and female mice exposed to HF diet, expression of mEGFP was reduced by > 40% in Sim1 neurons of the PVN, an effect paralleled by cell apoptosis and neuronal loss, but not by microgliosis. In the arcuate nucleus of the Sim1-Cre:Rosa-mEGFP male mice, there was decreased alpha-melanocyte-stimulating hormone in proopiomelanocortin neurons projecting to the PVN, with increased cell apoptosis, neuronal loss, and microgliosis. These defects were undetectable in the arcuate nucleus of female mice exposed to the HF diet. Thus, injury to Sim1 neurons of the PVN is a shared feature of exposure to HF diet in mice of both sexes, while injury to proopiomelanocortin neurons in arcuate nucleus is specific to male mice. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Eugene Nyamugenda
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Marcus Trentzsch
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Susan Russell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Tiffany Miles
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.,The Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kevin D Phelan
- Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Giulia Baldini
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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11
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Nishiumi S, Izumi Y, Yoshida M. Alterations in Docosahexaenoic Acid-Related Lipid Cascades in Inflammatory Bowel Disease Model Mice. Dig Dis Sci 2018; 63:1485-1496. [PMID: 29564669 DOI: 10.1007/s10620-018-5025-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/13/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is an intestinal disorder, involving chronic and relapsing inflammation of the digestive tract. Dysregulation of the immune system based on genetic, environmental, and other factors seems to be involved in the onset of IBD, but its exact pathogenesis remains unclear. Therefore, radical treatments for ulcerative colitis and Crohn's disease remain to be found, and IBD is considered to be a refractory disease. AIMS The aim of this study is to obtain novel insights into IBD via metabolite profiling of interleukin (IL)-10 knockout mice (an IBD animal model that exhibits a dysregulated immune system). METHODS In this study, the metabolites in the large intestine and plasma of IL-10 knockout mice were analyzed. In our analytical system, two kinds of analysis (gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry) were used to detect a broader range of metabolites, including both hydrophilic and hydrophobic metabolites. In addition, an analysis of lipid mediators in the large intestine and ascites of IL-10 knockout mice was carried out. RESULTS The levels of a variety of metabolites, including lipid mediators, were altered in IL-10 knockout mice. For example, high large intestinal and plasma levels of docosahexaenoic acid (DHA) were observed. In addition, arachidonic acid- and DHA-related lipid cascades were upregulated in the ascites of the IL-10 knockout mice. CONCLUSIONS Our findings based on metabolite profiles including lipid mediators must contribute to development of researches about IBD.
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Affiliation(s)
- Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.
| | - Yoshihiro Izumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.,Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan. .,Division of Metabolomics Research, Department of Internal Related, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan. .,AMED-CREST, AMED, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.
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12
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Tebani A, Afonso C, Bekri S. Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery. J Inherit Metab Dis 2018; 41:393-406. [PMID: 28842777 PMCID: PMC5959951 DOI: 10.1007/s10545-017-0080-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/11/2022]
Abstract
This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments.
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Affiliation(s)
- Abdellah Tebani
- Department of Metabolic Biochemistry, Rouen University Hospital, 76000, Rouen, France
- Normandie Université, UNIROUEN, CHU Rouen, IRIB, INSERM U1245, 76000, Rouen, France
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000, Rouen, France
| | - Carlos Afonso
- Normandie Université, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000, Rouen, France
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Rouen University Hospital, 76000, Rouen, France.
- Normandie Université, UNIROUEN, CHU Rouen, IRIB, INSERM U1245, 76000, Rouen, France.
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13
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Rustam YH, Reid GE. Analytical Challenges and Recent Advances in Mass Spectrometry Based Lipidomics. Anal Chem 2017; 90:374-397. [PMID: 29166560 DOI: 10.1021/acs.analchem.7b04836] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yepy H Rustam
- Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Gavin E Reid
- Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3010, Australia.,School of Chemistry, University of Melbourne , Parkville, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
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14
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Minami S, Yamamoto T, Takabatake Y, Takahashi A, Namba T, Matsuda J, Kimura T, Kaimori JY, Matsui I, Hamano T, Takeda H, Takahashi M, Izumi Y, Bamba T, Matsusaka T, Niimura F, Isaka Y. Lipophagy maintains energy homeostasis in the kidney proximal tubule during prolonged starvation. Autophagy 2017; 13:1629-1647. [PMID: 28813167 DOI: 10.1080/15548627.2017.1341464] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Macroautophagy/autophagy is a self-degradation process that combats starvation. Lipids are the main energy source in kidney proximal tubular cells (PTCs). During starvation, PTCs increase fatty acid (FA) uptake, form intracellular lipid droplets (LDs), and hydrolyze them for use. The involvement of autophagy in lipid metabolism in the kidney remains largely unknown. Here, we investigated the autophagy-mediated regulation of renal lipid metabolism during prolonged starvation using PTC-specific Atg5-deficient (atg5-TSKO) mice and an in vitro serum starvation model. Twenty-four h of starvation comparably induced LD formation in the PTCs of control and atg5-TSKO mice; however, additional 24 h of starvation reduced the number of LDs in control mice, whereas increases were observed in atg5-TSKO mice. Autophagic degradation of LDs (lipophagy) in PTCs was demonstrated by electron microscopic observation and biochemical analysis. In vitro pulse-chase assays demonstrated that lipophagy mobilizes FAs from LDs to mitochondria during starvation, whereas impaired LD degradation in autophagy-deficient PTCs led to decreased ATP production and subsequent cell death. In contrast to the in vitro assay, despite impaired LD degradation, kidney ATP content was preserved in 48-h starved atg5-TSKO mice, probably due to increased utilization of ketone bodies. This compensatory mechanism was accompanied by a higher plasma FGF21 (fibroblast growth factor 21) level and its expression in the PTCs; however, this was not essential for the production of ketone bodies in the liver during prolonged starvation. In conclusion, lipophagy combats prolonged starvation in PTCs to avoid cellular energy depletion.
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Affiliation(s)
- Satoshi Minami
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Takeshi Yamamoto
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Yoshitsugu Takabatake
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Atsushi Takahashi
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Tomoko Namba
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Jun Matsuda
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Tomonori Kimura
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Jun-Ya Kaimori
- b Department of Advanced Technology for Transplantation , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Isao Matsui
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Takayuki Hamano
- c Department of Comprehensive Kidney Disease Research (CKDR) , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Hiroaki Takeda
- d Division of Metabolomics, Medical Institute of Bioregulation , Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Masatomo Takahashi
- d Division of Metabolomics, Medical Institute of Bioregulation , Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Yoshihiro Izumi
- d Division of Metabolomics, Medical Institute of Bioregulation , Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Takeshi Bamba
- d Division of Metabolomics, Medical Institute of Bioregulation , Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Taiji Matsusaka
- e Institute of Medical Sciences and Department of Molecular Life Sciences , Tokai University School of Medicine , Isehara , Kanagawa , Japan
| | - Fumio Niimura
- f Department of Pediatrics , Tokai University School of Medicine , Isehara , Kanagawa , Japan
| | - Yoshitaka Isaka
- a Department of Nephrology , Osaka University Graduate School of Medicine , Suita , Osaka , Japan
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15
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Perez de Souza L, Naake T, Tohge T, Fernie AR. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 2017; 6:1-20. [PMID: 28520864 PMCID: PMC5499862 DOI: 10.1093/gigascience/gix037] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/19/2023] Open
Abstract
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway toward improving our coverage of the plant metabolome.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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16
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Ogawa T, Izumi Y, Kusumoto K, Fukusaki E, Bamba T. Wide target analysis of acylglycerols in miso (Japanese fermented soybean paste) by supercritical fluid chromatography coupled with triple quadrupole mass spectrometry and the analysis of the correlation between taste and both acylglycerols and free fatty acids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:928-936. [PMID: 28370582 DOI: 10.1002/rcm.7862] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/22/2017] [Accepted: 03/25/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE The acylglycerols in miso have not been studied although it is known that they are important to the taste. In order to determine the fatty acid constituents in the acylglycerols and analyze them individually, multiple reaction monitoring (MRM) was performed utilizing a single platform, typically using both gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry. METHODS Acylglycerols and fatty acids (FAs) in miso were extracted using the Bligh-Dyer method. Supercritical fluid chromatography (SFC) with a C30 column was conducted for separation, and mass spectrometric (MS) analysis was performed with electrospray ionization using a triple quadrupole mass spectrometer (QqQMS) in the MRM mode. RESULTS The detection of FAs from the hydrolysis of acylglycerols and individual acylglycerols was achieved using only an SFC/MS platform. From the quality control (QC) sample of miso, we determined the main FA constituents, and then performed wide target analysis using MRM. In total, 23 triacylglycerols, 10 diacylglycerols, two monoacylglycerols, and five FAs were annotated effectively. Furthermore, the important compounds related to taste were determined through the analysis using both the relative quantitative data of acylglycerols and FAs and the quantitative descriptive analysis data of miso. CONCLUSIONS A method for the determination of the FA constituents in acylglycerols after hydrolysis and the comprehensive analysis of acylglycerols and FAs using MRM with SFC/QqQMS was developed. Using the data from the comprehensive analysis of acylglycerols and quantitative descriptive data, the key compounds related to taste were investigated. This type of research on lipids and the taste of food is expected to progress hereafter. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Takahiro Ogawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Izumi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kenichi Kusumoto
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tusukuba, 305-8642, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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17
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The importance of bioinformatics for connecting data-driven lipidomics and biological insights. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:762-765. [PMID: 28514647 DOI: 10.1016/j.bbalip.2017.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/20/2022]
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18
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Goracci L, Tortorella S, Tiberi P, Pellegrino RM, Di Veroli A, Valeri A, Cruciani G. Lipostar, a Comprehensive Platform-Neutral Cheminformatics Tool for Lipidomics. Anal Chem 2017; 89:6257-6264. [DOI: 10.1021/acs.analchem.7b01259] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Sara Tortorella
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Paolo Tiberi
- Molecular Discovery Ltd., Centennial
Park, Borehamwood, Hertfordshire, United Kingdom
| | - Roberto Maria Pellegrino
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Alessandra Di Veroli
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Aurora Valeri
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
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19
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Yamada T, Bamba T. Lipid Profiling by Supercritical Fluid Chromatography/Mass Spectrometry. NEUROMETHODS 2017. [DOI: 10.1007/978-1-4939-6946-3_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Cajka T, Fiehn O. Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics. Anal Chem 2015; 88:524-45. [PMID: 26637011 DOI: 10.1021/acs.analchem.5b04491] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomas Cajka
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States
| | - Oliver Fiehn
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States.,King Abdulaziz University , Faculty of Science, Biochemistry Department, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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