1
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Bo Y, Yu Q, Gao W. Progress of depression mechanism based on Omics method. J Pharm Biomed Anal 2024; 240:115884. [PMID: 38183729 DOI: 10.1016/j.jpba.2023.115884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 01/08/2024]
Abstract
Depression is a very common disabling mental disorder, which is typically characterized by high rates of disability and mortality. Although research into the various mechanisms of depression was still underway, its physiopathology remains uncertain. The rapid developments in new technologies and the combined use of a variety of techniques will help to understand the pathogenesis of depression and explore effective treatment methods. In this review, we focus on the combination of proteomic and metabolomic approaches to analyze metabolites and proteins in animal models of depression induced by different modeling approaches, with the aim of broadening the understanding of the physiopathological mechanisms of depression using complementary "omics" strategy.
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Affiliation(s)
- Yaping Bo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, PR China
| | - Qing Yu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, PR China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, PR China.
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2
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Hartung NM, Mainka M, Pfaff R, Kuhn M, Biernacki S, Zinnert L, Schebb NH. Development of a quantitative proteomics approach for cyclooxygenases and lipoxygenases in parallel to quantitative oxylipin analysis allowing the comprehensive investigation of the arachidonic acid cascade. Anal Bioanal Chem 2023; 415:913-933. [PMID: 36683060 PMCID: PMC9883352 DOI: 10.1007/s00216-022-04489-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Oxylipins derived from the cyclooxygenase (COX) and lipoxygenase (LOX) pathways of the arachidonic acid (ARA) cascade are essential for the regulation of the inflammatory response and many other physiological functions. Comprehensive analytical methods comprised of oxylipin and protein abundance analysis are required to fully understand mechanisms leading to changes within these pathways. Here, we describe the development of a quantitative multi-omics approach combining liquid chromatography tandem mass spectrometry-based targeted oxylipin metabolomics and proteomics. As the first targeted proteomics method to cover these pathways, it enables the quantitative analysis of all human COX (COX-1 and COX-2) and relevant LOX pathway enzymes (5-LOX, 12-LOX, 15-LOX, 15-LOX-2, and FLAP) in parallel to the analysis of 239 oxylipins with our targeted oxylipin metabolomics method from a single sample. The detailed comparison between MRM3 and classical MRM-based detection in proteomics showed increased selectivity for MRM3, while MRM performed better in terms of sensitivity (LLOQ, 16-122 pM vs. 75-840 pM for the same peptides), linear range (up to 1.5-7.4 μM vs. 4-368 nM), and multiplexing capacities. Thus, the MRM mode was more favorable for this pathway analysis. With this sensitive multi-omics approach, we comprehensively characterized oxylipin and protein patterns in the human monocytic cell line THP-1 and differently polarized primary macrophages. Finally, the quantification of changes in protein and oxylipin levels induced by lipopolysaccharide stimulation and pharmaceutical treatment demonstrates its usefulness to study molecular modes of action involved in the modulation of the ARA cascade.
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Affiliation(s)
- Nicole M Hartung
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Malwina Mainka
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Rebecca Pfaff
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Michael Kuhn
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Sebastian Biernacki
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Lilli Zinnert
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany.
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3
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Steinmetz-Späh J, Liu J, Singh R, Ekoff M, Boddul S, Tang X, Bergqvist F, Idborg H, Heitel P, Rönnberg E, Merk D, Wermeling F, Haeggström JZ, Nilsson G, Steinhilber D, Larsson K, Korotkova M, Jakobsson PJ. Biosynthesis of prostaglandin 15dPGJ 2 -glutathione and 15dPGJ 2-cysteine conjugates in macrophages and mast cells via MGST3. J Lipid Res 2022; 63:100310. [PMID: 36370807 PMCID: PMC9792570 DOI: 10.1016/j.jlr.2022.100310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
Inhibition of microsomal prostaglandin E synthase-1 (mPGES-1) results in decreased production of proinflammatory PGE2 and can lead to shunting of PGH2 into the prostaglandin D2 (PGD2)/15-deoxy-Δ12,14-prostaglandin J2 (15dPGJ2) pathway. 15dPGJ2 forms Michael adducts with thiol-containing biomolecules such as GSH or cysteine residues on target proteins and is thought to promote resolution of inflammation. We aimed to elucidate the biosynthesis and metabolism of 15dPGJ2 via conjugation with GSH, to form 15dPGJ2-glutathione (15dPGJ2-GS) and 15dPGJ2-cysteine (15dPGJ2-Cys) conjugates and to characterize the effects of mPGES-1 inhibition on the PGD2/15dPGJ2 pathway in mouse and human immune cells. Our results demonstrate the formation of PGD2, 15dPGJ2, 15dPGJ2-GS, and 15dPGJ2-Cys in RAW264.7 cells after lipopolysaccharide stimulation. Moreover, 15dPGJ2-Cys was found in lipopolysaccharide-activated primary murine macrophages as well as in human mast cells following stimulation of the IgE-receptor. Our results also suggest that the microsomal glutathione S-transferase 3 is essential for the formation of 15dPGJ2 conjugates. In contrast to inhibition of cyclooxygenase, which leads to blockage of the PGD2/15dPGJ2 pathway, we found that inhibition of mPGES-1 preserves PGD2 and its metabolites. Collectively, this study highlights the formation of 15dPGJ2-GS and 15dPGJ2-Cys in mouse and human immune cells, the involvement of microsomal glutathione S-transferase 3 in their biosynthesis, and their unchanged formation following inhibition of mPGES-1. The results encourage further research on their roles as bioactive lipid mediators.
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Affiliation(s)
- Julia Steinmetz-Späh
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jianyang Liu
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Rajkumar Singh
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Ekoff
- Division of Immunology and Allergy, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sanjaykumar Boddul
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Xiao Tang
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Filip Bergqvist
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Helena Idborg
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Elin Rönnberg
- Division of Immunology and Allergy, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Fredrik Wermeling
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Z. Haeggström
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Nilsson
- Division of Immunology and Allergy, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Karin Larsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Marina Korotkova
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden,For correspondence: Per-Johan Jakobsson
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4
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Brace N, Megson IL, Rossi AG, Doherty MK, Whitfield PD. SILAC-based quantitative proteomics to investigate the eicosanoid associated inflammatory response in activated macrophages. J Inflamm (Lond) 2022; 19:12. [PMID: 36050729 PMCID: PMC9438320 DOI: 10.1186/s12950-022-00309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Macrophages play a central role in inflammation by phagocytosing invading pathogens, apoptotic cells and debris, as well as mediating repair of tissues damaged by trauma. In order to do this, these dynamic cells generate a variety of inflammatory mediators including eicosanoids such as prostaglandins, leukotrienes and hydroxyeicosatraenoic acids (HETEs) that are formed through the cyclooxygenase, lipoxygenase and cytochrome P450 pathways. The ability to examine the effects of eicosanoid production at the protein level is therefore critical to understanding the mechanisms associated with macrophage activation. RESULTS This study presents a stable isotope labelling with amino acids in cell culture (SILAC) -based proteomics strategy to quantify the changes in macrophage protein abundance following inflammatory stimulation with Kdo2-lipid A and ATP, with a focus on eicosanoid metabolism and regulation. Detailed gene ontology analysis, at the protein level, revealed several key pathways with a decrease in expression in response to macrophage activation, which included a promotion of macrophage polarisation and dynamic changes to energy requirements, transcription and translation. These findings suggest that, whilst there is evidence for the induction of a pro-inflammatory response in the form of prostaglandin secretion, there is also metabolic reprogramming along with a change in cell polarisation towards a reduced pro-inflammatory phenotype. CONCLUSIONS Advanced quantitative proteomics in conjunction with functional pathway network analysis is a useful tool to investigate the molecular pathways involved in inflammation.
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Affiliation(s)
- Nicole Brace
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK
| | - Ian L Megson
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK
| | - Adriano G Rossi
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mary K Doherty
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK
| | - Phillip D Whitfield
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK.
- Present Address: Glasgow Polyomics, Garscube Campus, University of Glasgow, Glasgow, G61 1BD, UK.
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5
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Martínez-Torró C, Torres-Puig S, Marcos-Silva M, Huguet-Ramón M, Muñoz-Navarro C, Lluch-Senar M, Serrano L, Querol E, Piñol J, Pich OQ. Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium. Front Microbiol 2021; 12:695572. [PMID: 34589065 PMCID: PMC8475190 DOI: 10.3389/fmicb.2021.695572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/10/2021] [Indexed: 12/03/2022] Open
Abstract
It is well-established that FtsZ drives peptidoglycan synthesis at the division site in walled bacteria. However, the function and conservation of FtsZ in wall-less prokaryotes such as mycoplasmas are less clear. In the genome-reduced bacterium Mycoplasma genitalium, the cell division gene cluster is limited to four genes: mraZ, mraW, MG_223, and ftsZ. In a previous study, we demonstrated that ftsZ was dispensable for growth of M. genitalium under laboratory culture conditions. Herein, we show that the entire cell division gene cluster of M. genitalium is non-essential for growth in vitro. Our analyses indicate that loss of the mraZ gene alone is more detrimental for growth of M. genitalium than deletion of ftsZ or the entire cell division gene cluster. Transcriptional analysis revealed a marked upregulation of ftsZ in the mraZ mutant. Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics confirmed the overexpression of FtsZ in MraZ-deprived cells. Of note, we found that ftsZ expression was upregulated in non-adherent cells of M. genitalium, which arise spontaneously at relatively high rates. Single cell analysis using fluorescent markers showed that FtsZ localization varied throughout the cell cycle of M. genitalium in a coordinated manner with the chromosome and the terminal organelle (TMO). In addition, our results indicate a possible role for the RNA methyltransferase MraW in the regulation of FtsZ expression at the post-transcriptional level. Altogether, this study provides an extensive characterization of the cell division gene cluster of M. genitalium and demonstrates the existence of regulatory elements controlling FtsZ expression at the temporal and spatial level in mycoplasmas.
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Affiliation(s)
- Carlos Martínez-Torró
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Torres-Puig
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina Marcos-Silva
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Huguet-Ramón
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Navarro
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar Q. Pich
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d’Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Sabadell, Spain
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6
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Hartung NM, Ostermann AI, Immenschuh S, Schebb NH. Combined Targeted Proteomics and Oxylipin Metabolomics for Monitoring of the COX-2 Pathway. Proteomics 2020; 21:e1900058. [PMID: 32875715 DOI: 10.1002/pmic.201900058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/25/2020] [Indexed: 12/21/2022]
Abstract
The important role of inducible cyclooxygenase-2 (COX-2) in several diseases necessitates analytical tools enabling thorough understanding of its modulation. Analysis of a comprehensive oxylipin pattern provides detailed information about changes in enzyme activities. In order to simultaneously monitor gene expression levels, a targeted proteomics method for human COX-2 is developed. With limits of detection and quantification down to 0.25 and 0.5 fmol (on column) the method enables sensitive quantitative analysis via LC-MS/MS within a linear range up to 2.5 pmol. Three housekeeping proteins are included in the method for data normalization. A tiered approach for method development comprised of in silico and experimental steps is described for choosing unique peptides and selective and sensitive SRM transitions while avoiding isobaric interferences. This method combined with a well-established targeted oxylipin metabolomics method allows to investigate the role of COX-2 in the human colon carcinoma cell lines HCT-116, HT-29, and HCA-7. Moreover, the developed methodology is used to demonstrate the time-dependent prostanoid formation and COX-2 enzyme synthesis in lipopolysaccharide-stimulated human primary macrophages. The described approach is a helpful tool which will be further used as standard operation procedure, ultimately aiming at comprehensive targeted proteomics/oxylipin metabolomics strategies to examine the entire arachidonic acid cascade.
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Affiliation(s)
- Nicole M Hartung
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, Wuppertal, 42119, Germany
| | - Annika I Ostermann
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, Wuppertal, 42119, Germany
| | - Stephan Immenschuh
- Institute for Transfusion Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
| | - Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, Wuppertal, 42119, Germany
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7
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Rodríguez-Blanco G, Zeneyedpour L, Duijvesz D, Hoogland AM, Verhoef EI, Kweldam CF, Burgers PC, Smitt PS, Bangma CH, Jenster G, van Leenders GJLH, Dekker LJM, Luider TM. Tissue proteomics outlines AGR2 AND LOX5 as markers for biochemical recurrence of prostate cancer. Oncotarget 2018; 9:36444-36456. [PMID: 30559929 PMCID: PMC6284859 DOI: 10.18632/oncotarget.26342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/21/2018] [Indexed: 12/22/2022] Open
Abstract
Although many patients are cured from prostate cancer (PCa) by surgery only, there are still patients who will experience rising prostate-specific antigen (PSA) levels after surgery, a condition known as biochemical recurrence (BCR). Novel protein prognostic markers in PCa tissue might enable finding better treatment for those patients experiencing BCR with a high chance of metastasis. In this study, we aimed to identify altered proteins in prostate cancer tissue, and to evaluate their potential role as prognostic markers. We used two proteomics strategies to analyse 34 prostate tumours (PCa) and 33 normal adjacent prostate (NAP) tissues. An independent cohort of 481 samples was used to evaluate the expression of three proteins: AGR2, FASN and LOX5 as prognostic markers of the disease. Tissue microarray immunohistochemical staining indicated that a low percentage of positive tumour cells for AGR2 (HR (95% CI) = 0.61 (0.43-0.93)), and a low percentage of positive tumour cells for LOX5 expression (HR (95% CI) = 2.53 (1.23-5.22)) are predictors of BCR after RP. In contrast, FASN expression had no prognostic value for PCa.
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Affiliation(s)
| | - Lona Zeneyedpour
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Diederick Duijvesz
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - A Marije Hoogland
- Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Esther I Verhoef
- Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Peter C Burgers
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Chris H Bangma
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Lennard J M Dekker
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
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Abstract
The quantification of eicosanoids and their metabolites in biological samples remain an analytical challenge, even though a number of methodologies/techniques have been developed. The major difficulties encountered are related to the oxidation of eicosanoids and their low quantities in biological matrices. Among the known methodologies, liquid chromatography-mass spectrometry (LC-MS/MS) is the standard method for eicosanoid quantification in biological samples. Recently advances have improved the ability to identify and simultaneous quantitate eicosanoids in biological matrices. The present article reviews the quantitative analysis of eicosanoids in different biological matrices by LC and ultra performance liquid chromatography (UPLC)-MS/MS and discusses important aspects to be considered during the collection, sample preparation and the generation of calibration curves required for eicosanoid analysis.
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9
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Belužić L, Grbeša I, Belužić R, Park JH, Kong HK, Kopjar N, Espadas G, Sabidó E, Lepur A, Rokić F, Jerić I, Brkljačić L, Vugrek O. Knock-down of AHCY and depletion of adenosine induces DNA damage and cell cycle arrest. Sci Rep 2018; 8:14012. [PMID: 30228286 DOI: 10.1038/s41598-018-32356-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/03/2018] [Indexed: 01/09/2023] Open
Abstract
Recently, functional connections between S-adenosylhomocysteine hydrolase (AHCY) activity and cancer have been reported. As the properties of AHCY include the hydrolysis of S-adenosylhomocysteine and maintenance of the cellular methylation potential, the connection between AHCY and cancer is not obvious. The mechanisms by which AHCY influences the cell cycle or cell proliferation have not yet been confirmed. To elucidate AHCY-driven cancer-specific mechanisms, we pursued a multi-omics approach to investigate the effect of AHCY-knockdown on hepatocellular carcinoma cells. Here, we show that reduced AHCY activity causes adenosine depletion with activation of the DNA damage response (DDR), leading to cell cycle arrest, a decreased proliferation rate and DNA damage. The underlying mechanism behind these effects might be applicable to cancer types that have either significant levels of endogenous AHCY and/or are dependent on high concentrations of adenosine in their microenvironments. Thus, adenosine monitoring might be used as a preventive measure in liver disease, whereas induced adenosine depletion might be the desired approach for provoking the DDR in diagnosed cancer, thus opening new avenues for targeted therapy. Additionally, including AHCY in mutational screens as a potential risk factor may be a beneficial preventive measure.
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10
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Wang D, Sun X, Yan J, Ren B, Cao B, Lu Q, Liu Y, Zeng J, Huang N, Xie Q, Gu H, Wang J. Alterations of eicosanoids and related mediators in patients with schizophrenia. J Psychiatr Res 2018; 102:168-78. [PMID: 29674269 DOI: 10.1016/j.jpsychires.2018.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/22/2018] [Accepted: 04/04/2018] [Indexed: 02/08/2023]
Abstract
Schizophrenia (SCZ) is a multifactorial psychiatric disorder. Currently, its molecular pathogenesis remains largely unknown, and no reliable test for diagnosis and therapy monitoring is available. Polyunsaturated fatty acids (PUFAs) and their derived eicosanoid signaling abnormalities are relevant to the pathophysiology of schizophrenia. However, comprehensive analysis of eicosanoids and related mediators for schizophrenia is very rare. In this study, we applied a targeted liquid chromatography-mass spectrometry based method to monitor 158 PUFAs, eicosanoids and related mediators from enzyme-dependent or independent pathways, in the serum samples of 109 healthy controls, and 115 schizophrenia patients at baseline and after an 8-week period of antipsychotic therapy. Twenty-three metabolites were identified to be significantly altered in SCZ patients at baseline compared to healthy controls, especially arachidonic acid (AA) derived eicosanoids. These disturbances may be related to altered immunological reactions and neurotransmitter signaling. After 8-week antipsychotic treatment, there were 22 metabolites, especially AA and linoleic acid derived eicosanoids, significantly altered in posttreatment patients. Some metabolites, such as several AA derived prostaglandins, thromboxanes, and di-hydroxy-eicosatrienoic acids were reversed toward normal levels after treatment. Based on univariate analysis and orthogonal partial least-squares discriminant analysis, anandamide, oleoylethanolamine, and AA were selected as a panel of potential biomarkers for differentiating baseline SCZ patients from controls, which showed a high sensitivity (0.907), good specificity (0.843) and excellent area under the receiver operating characteristic curve (0.940). This study provided a new perspective to understand the pathophysiological mechanism and identify potential biomarkers of SCZ.
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11
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Abstract
Mass spectrometry-based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label-based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling-based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.
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Affiliation(s)
- J Astor Ankney
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Adil Muneer
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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12
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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13
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Zhao H, Du H, Liu M, Gao S, Li N, Chao Y, Li R, Chen W, Lou Z, Dong X. Integrative Proteomics-Metabolomics Strategy for Pathological Mechanism of Vascular Depression Mouse Model. J Proteome Res 2017; 17:656-669. [PMID: 29190102 DOI: 10.1021/acs.jproteome.7b00724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Vascular depression (VD), a subtype of depression, is caused by vascular diseases or cerebrovascular risk factors. Recently, the proportion of VD patients has increased significantly, which severely affects their quality of life. However, the current pathogenesis of VD has not yet been fully understood, and the basic research is not adequate. In this study, on the basis of the combination of LC-MS-based proteomics and metabolomics, we aimed to establish a protein metabolism regulatory network in a murine VD model to elucidate a more comprehensive impact of VD on organisms. We detected 44 metabolites and 304 proteins with different levels in the hippocampus samples from VD mice using a combination of metabolomic and proteomics analyses with an isobaric tags for relative and absolute quantification (iTRAQ) method. We constructed a protein-to-metabolic regulatory network by correlating and integrating the differential metabolites and proteins using ingenuity pathway analysis. Then we quantitatively validated the levels of the bimolecules shown in the bioinformatics analysis using LC-MS/MS and Western blotting. Validation results suggested changes in the regulation of neuroplasticity, transport of neurotransmitters, neuronal cell proliferation and apoptosis, and disorders of amino acids, lipids and energy metabolism. These proteins and metabolites involved in these dis-regulated pathways will provide a more targeted and credible direction to study the mechanism of VD. Therefore, this paper presents an approach and strategy that was applied in integrative proteomics and metabolomics for research and screening potential targets and biomarkers of VD, which could be more precise and credible in a field lacking adequate basic research.
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Affiliation(s)
- Hongxia Zhao
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Hongli Du
- Department of Pharmacy, Eastern Hepatobiliary Surgery Hospital , Shanghai 200433, China
| | - Min Liu
- Pharmacy Department of Changhai Hospital, Second Military Medical University , Shanghai 200433, China
| | - Songyan Gao
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Na Li
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Yufan Chao
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Ruiqing Li
- School of Life Sciences and Technology, Shanghai Tech University , Shanghai 200433, China
| | - Wei Chen
- Changhai Hospital, Second Military Medical University , Shanghai 200433, China
| | - Ziyang Lou
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Xin Dong
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
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14
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Abstract
Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.
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Affiliation(s)
- Ting Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
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15
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Abstract
In 1970, it was well accepted that the central role of lipids was in energy storage and metabolism, and it was assumed that amphipathic lipids simply served a passive structural role as the backbone of biological membranes. As a result, the scientific community was focused on nucleic acids, proteins, and carbohydrates as information-containing molecules. It took considerable effort until scientists accepted that lipids also "encode" specific and unique biological information and play a central role in cell signaling. Along with this realization came the recognition that the enzymes that act on lipid substrates residing in or on membranes and micelles must also have important signaling roles, spurring curiosity into their potentially unique modes of action differing from those acting on water-soluble substrates. This led to the creation of the concept of "surface dilution kinetics" for describing the mechanism of enzymes acting on lipid substrates, as well as the demonstration that lipid enzymes such as phospholipase A2 (PLA2) contain allosteric activator sites for specific phospholipids as well as for membranes. As our understanding of phospholipases advanced, so did the understanding that many of the lipids released by these enzymes are chiral information-containing signaling molecules; for example, PLA2 regulates the generation of precursors for the biosynthesis of eicosanoids and other bioactive lipid mediators of inflammation and resolution underlying disease progression. The creation of the LIPID MAPS initiative in 2003 and the ensuing development of the lipidomics field have revealed that lipid metabolites are central to human metabolism. Today lipids are recognized as key mediators of health and disease as we enter a new era of biomarkers and personalized medicine. This article is my personal "reflection" on these scientific advances.
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Affiliation(s)
- Edward A Dennis
- From the Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California 92093-0601.
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16
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Cao H, Zhang A, Sun H, Zhou X, Guan Y, Liu Q, Kong L, Wang X. Metabolomics-proteomics profiles delineate metabolic changes in kidney fibrosis disease. Proteomics 2016; 15:3699-710. [PMID: 26256572 DOI: 10.1002/pmic.201500062] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 07/16/2015] [Accepted: 08/06/2015] [Indexed: 12/24/2022]
Abstract
Kidney fibrosis (KF) is a common process that leads to the progression of various types of kidney disease including kidney-yang deficiency syndrome, however, little is known regarding the underlying biology of this disorder. Fortunately, integrated omics approaches provide the molecule fingerprints related to the disease. In an attempt to address this issue, we integrated metabolomics-proteomics profiles analyzed pathogenic mechanisms of KF based on rat model. A total 37 serum differential metabolites were contributed to KF progress, involved several important metabolic pathways. Using iTRAQ-based quantitative proteomics analysis, 126 differential serum proteins were identified and provide valuable insight into the underlying mechanisms of KF. These proteins appear to be involved in complement and coagulation cascades, regulation of actin cytoskeleton, MAPK signaling pathway, RNA transport, etc. Interestingly, pathway/network analysis of integrated proteomics and metabolomics data firstly reveals that these signaling pathways were closely related with KF. It further indicated that most of these proteins play a pivotal role in the regulation of metabolism pathways.
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Affiliation(s)
- Hongxin Cao
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China.,China Academy of Chinese Medical Science, Beijing, P. R. China
| | - Aihua Zhang
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Hui Sun
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Xiaohang Zhou
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Yu Guan
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Qi Liu
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Ling Kong
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Xijun Wang
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
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17
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Casanovas A, Sprenger RR, Tarasov K, Ruckerbauer DE, Hannibal-Bach HK, Zanghellini J, Jensen ON, Ejsing CS. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism. ACTA ACUST UNITED AC 2016; 22:412-25. [PMID: 25794437 DOI: 10.1016/j.chembiol.2015.02.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 02/20/2015] [Accepted: 02/22/2015] [Indexed: 12/24/2022]
Abstract
Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular architecture and processes during physiological adaptations in yeast. Our results reveal that activation of cardiolipin synthesis and remodeling supports mitochondrial biogenesis in the transition from fermentative to respiratory metabolism, that down-regulation of de novo sterol synthesis machinery prompts differential turnover of lipid droplet-associated triacylglycerols and sterol esters during respiratory growth, that sphingolipid metabolism is regulated in a previously unrecognized growth stage-specific manner, and that endogenous synthesis of unsaturated fatty acids constitutes an in vivo upstream activator of peroxisomal biogenesis, via the heterodimeric Oaf1/Pip2 transcription factor. Our work demonstrates the pivotal role of lipid metabolism in adaptive processes and provides a resource to investigate its regulation at the cellular level.
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Affiliation(s)
- Albert Casanovas
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Kirill Tarasov
- Département de Biochimie, Université de Montréal, Succ. Centre-Ville, 6128 Montreal, Quebec H3C 3J7, Canada
| | - David E Ruckerbauer
- Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Hans Kristian Hannibal-Bach
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Jürgen Zanghellini
- Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
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18
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Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R. Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology. Mol Cell Proteomics 2016; 15:1453-66. [PMID: 26814187 DOI: 10.1074/mcp.m115.053702] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 11/06/2022] Open
Abstract
Interconnected molecular networks are at the heart of signaling pathways that mediate adaptive plasticity of eukaryotic cells. To gain deeper insights into the underlying molecular mechanisms, a comprehensive and representative analysis demands a deep and parallel coverage of a broad spectrum of molecular species. Therefore, we introduce a simultaneous metabolite, protein, lipid extraction (SIMPLEX) procedure, a novel strategy for the quantitative investigation of lipids, metabolites, and proteins. Compared with unimolecular workflows, SIMPLEX offers a fundamental turn in study design since multiple molecular classes can be accessed in parallel from one sample with equal efficiency and reproducibility. Application of this method in mass-spectrometry-based workflows allowed the simultaneous quantification of 360 lipids, 75 metabolites, and 3327 proteins from 10(6)cells. The versatility of this method is shown in a model system for adipogenesis- peroxisomal proliferator-activated receptor gamma (PPARG) signaling in mesenchymal stem cells-where we utilized SIMPLEX to explore cross-talk within and between all three molecular classes and identified novel potential molecular entry points for interventions, indicating that SIMPLEX provides a superior strategy compared with conventional workflows.
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Affiliation(s)
- Cristina Coman
- ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK
| | - Fiorella Andrea Solari
- ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK
| | - Andreas Hentschel
- ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK
| | - Albert Sickmann
- ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK
| | - René Peiman Zahedi
- ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK
| | - Robert Ahrends
- ‖College of Physical Sciences, University of Aberdeen, Department of Chemistry, Aberdeen, UK
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19
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Zhang A, Yan G, Zhou X, Wang Y, Han Y, Guan Y, Sun H, Wang X. High resolution metabolomics technology reveals widespread pathway changes of alcoholic liver disease. Mol BioSyst 2016; 12:262-73. [DOI: 10.1039/c5mb00603a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The current study provides insights into the molecular mechanisms of ALD from widespread pathway changes.
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Affiliation(s)
- Aihua Zhang
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Guangli Yan
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Xiaohang Zhou
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Yangyang Wang
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Ying Han
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Yu Guan
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Hui Sun
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Xijun Wang
- National TCM Key Laboratory of Serum Pharmacochemistry
- Laboratory of Metabolomics
- Research Center of Chinmedomics
- Heilongjiang University of Chinese Medicine
- Harbin 150040
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20
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Xue SS, He JL, Zhang X, Liu YJ, Xue FX, Wang CJ, Ai D, Zhu Y. Metabolomic analysis revealed the role of DNA methylation in the balance of arachidonic acid metabolism and endothelial activation. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1317-26. [DOI: 10.1016/j.bbalip.2015.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/19/2015] [Accepted: 07/06/2015] [Indexed: 01/26/2023]
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21
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Sun H, Wang H, Zhang A, Yan G, Zhang Y, An N, Wang X. Berberine ameliorates nonbacterial prostatitis via multi-target metabolic network regulation. OMICS 2015; 19:186-95. [PMID: 25588034 DOI: 10.1089/omi.2014.0112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metabolomics has been increasingly applied to discovering biomarkers and identifying perturbed pathways. Berberine has been shown to exhibit anti-inflammatory, antioxidant, and anticancer properties, but its mechanisms for treating nonbacterial prostatitis (NBP) remain unclear completely. We developed the untargeted metabolomics approach based on UPLC-Q-TOF-HDMS to profile the metabolite changes in urine samples in order to discover novel potential biomarkers to clarify mechanisms of berberine in treating a rat model of capsaicin-induced nonbacterial prostatitis (NBP). The changes in metabolic profiling were restored to their base-line values after berberine treatment according to the principal component analysis (PCA) score plots. Fourteen different potential biomarkers and five acutely perturbed metabolic pathways contributing to the treatment of NBP were discovered and identified. Specifically, the berberine-treated rats are located closer to the normal group, indicating that the NBP-induced disturbances to the metabolic profile were partially reversed by berberine treatment. After treatment with berberine, the relative contents of 12 potential biomarkers were effectively regulated, which suggested that the therapeutic effects of berberine on NBP may involve regulating disturbances to the metabolism. Our results show that the protective effect of berberine occurs in part through a reversal of the NBP-caused disturbances.
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Affiliation(s)
- Hui Sun
- National TCM Key Laboratory of Serum Pharmacochemistry, Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine , Harbin, China
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22
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Kihara Y, Gupta S, Maurya MR, Armando A, Shah I, Quehenberger O, Glass CK, Dennis EA, Subramaniam S. Modeling of eicosanoid fluxes reveals functional coupling between cyclooxygenases and terminal synthases. Biophys J 2014; 106:966-75. [PMID: 24559999 DOI: 10.1016/j.bpj.2014.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/27/2013] [Accepted: 01/10/2014] [Indexed: 12/11/2022] Open
Abstract
Eicosanoids, including prostaglandins (PG) and leukotrienes, are lipid mediators derived from arachidonic acid. A quantitative and biochemical level understanding of eicosanoid metabolism would aid in understanding the mechanisms that govern inflammatory processes. Here, we present a combined experimental and computational approach to understanding the biochemical basis of eicosanoid metabolism in macrophages. Lipidomic and transcriptomic measurements and analyses reveal temporal and dynamic changes of the eicosanoid metabolic network in mouse bone marrow-derived macrophages (BMDM) upon stimulation of the Toll-like receptor 4 with Kdo2-Lipid A (KLA) and stimulation of the P2X7 purinergic receptor with adenosine 5'-triphosphate. Kinetic models were developed for the cyclooxygenase (COX) and lipoxygenase branches of arachidonic acid metabolism, and then the rate constants were estimated with a data set from ATP-stimulated BMDM, using a two-step matrix-based approach employing a constrained least-squares method followed by nonlinear optimization. The robustness of the model was validated through parametric sensitivity, uncertainty analysis, and predicting an independent dataset from KLA-primed ATP-stimulated BMDM by allowing the parameters to vary within the uncertainty range of the calculated parameters. We analyzed the functional coupling between COX isozymes and terminal enzymes by developing a PGH2-divided model. This provided evidence for the functional coupling between COX-2 and PGE2 synthase, between COX-1/COX-2 and PGD2 synthase, and also between COX-1 and thromboxane A2 synthase. Further, these functional couplings were experimentally validated using COX-1 and COX-2 selective inhibitors. The resulting fluxomics analysis demonstrates that the "multi-omics" systems biology approach can define the complex machinery of eicosanoid networks.
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Affiliation(s)
- Yasuyuki Kihara
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California; Department of Bioengineering, University of California at San Diego, La Jolla, California
| | - Shakti Gupta
- Department of Bioengineering, University of California at San Diego, La Jolla, California
| | - Mano R Maurya
- Department of Bioengineering, University of California at San Diego, La Jolla, California
| | - Aaron Armando
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California
| | - Ishita Shah
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California
| | - Oswald Quehenberger
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California; Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, California
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California
| | - Edward A Dennis
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California.
| | - Shankar Subramaniam
- Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California; Department of Bioengineering, University of California at San Diego, La Jolla, California; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California.
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23
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Chiva C, Ortega M, Sabidó E. Influence of the digestion technique, protease, and missed cleavage peptides in protein quantitation. J Proteome Res 2014; 13:3979-86. [PMID: 24986539 DOI: 10.1021/pr500294d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Quantitative determination of absolute and relative protein amounts is an essential requirement for most current bottom-up proteomics applications, but protein quantitation estimates are affected by several sources of variability such as sample preparation, mass spectrometric acquisition, and data analysis. Among them, sample digestion has attracted much attention from the proteomics community, as protein quantitation by bottom-up proteomics relies on the efficiency and reproducibility of protein enzymatic digestion, with the presence of missed cleavages, nonspecific cleavages, or even the use of different proteases having been postulated as important sources of variation in protein quantitation. Here we evaluated both in-solution and filter-aided digestion protocols and assessed their influence in the estimation of protein abundances using five E. coli mixtures with known amounts of spiked proteins. We observed that replicates of trypsin specificity digestion protocols are highly reproducible in terms of peptide quantitation, with digestion technique and the chosen proteolytic enzyme being the major sources of variability in peptide quantitation. Finally, we also evaluated the result of including peptides with missed cleavages in protein quantitation and observed no significant differences in precision, accuracy, specificity, and sensitivity compared with the use of fully tryptic peptides.
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Affiliation(s)
- Cristina Chiva
- Proteomics Unit, Centre de Regulació Genòmica (CRG) , Dr. Aiguader 88, 08003 Barcelona, Spain
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24
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Montague E, Stanberry L, Higdon R, Janko I, Lee E, Anderson N, Choiniere J, Stewart E, Yandl G, Broomall W, Kolker N, Kolker E. MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. OMICS 2014; 18:335-43. [PMID: 24910945 PMCID: PMC4048574 DOI: 10.1089/omi.2014.0061] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org ) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org ) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding.
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Affiliation(s)
- Elizabeth Montague
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Larissa Stanberry
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Roger Higdon
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Imre Janko
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Elaine Lee
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Nathaniel Anderson
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - John Choiniere
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Elizabeth Stewart
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Gregory Yandl
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - William Broomall
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Natali Kolker
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
| | - Eugene Kolker
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, Washington
- Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington, Seattle, Washington
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25
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Chang CY, Sabidó E, Aebersold R, Vitek O. Targeted protein quantification using sparse reference labeling. Nat Methods 2014; 11:301-4. [DOI: 10.1038/nmeth.2806] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 12/13/2013] [Indexed: 12/22/2022]
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Liu S, Chen X, Yan Z, Qin S, Xu J, Lin J, Yang C, Shui W. Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules. Proteomics 2014; 14:169-80. [DOI: 10.1002/pmic.201300352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/26/2013] [Accepted: 11/19/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Shanshan Liu
- College of Life Sciences; Nankai University; Tianjin P. R. China
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
| | - Xin Chen
- College of Life Sciences; Nankai University; Tianjin P. R. China
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
| | - Zhihui Yan
- College of Life Sciences; Nankai University; Tianjin P. R. China
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
| | - Shanshan Qin
- College of Life Sciences; Nankai University; Tianjin P. R. China
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
| | - Jinhua Xu
- College of Life Sciences; Nankai University; Tianjin P. R. China
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
| | - Jianping Lin
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Nankai University; Tianjin P. R. China
| | - Cheng Yang
- High-Throughput Molecular Drug Discovery Center; Tianjin Joint Academy of Biotechnology and Medicine; Tianjin P. R. China
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Nankai University; Tianjin P. R. China
| | - Wenqing Shui
- College of Life Sciences; Nankai University; Tianjin P. R. China
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin P. R. China
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Abstract
Bioactive lipid mediators play crucial roles in promoting the induction and resolution of inflammation. Eicosanoids and other related unsaturated fatty acids have long been known to induce inflammation. These signaling molecules can modulate the circulatory system and stimulate immune cell infiltration into the site of infection. Recently, DHA- and EPA-derived metabolites have been discovered to promote the resolution of inflammation, an active process. Not only do these molecules stop the further infiltration of immune cells, they prompt non-phlogistic phagocytosis of apoptotic neutrophils, stimulating the tissue to return to homeostasis. After the rapid release of lipid precursors from the plasma membrane upon stimulation, families of enzymes in a complex network metabolize them to produce a large array of lipid metabolites. With current advances in mass spectrometry, the entire lipidome can be accurately quantified to assess the immune response upon microbial infection. In this review, we discuss the various lipid metabolism pathways in the context of the immune response to microbial pathogens, as well as their complex network interactions. With the advancement of mass spectrometry, these approaches have also been used to characterize the lipid mediator response of macrophages and neutrophils upon immune stimulation in vitro. Lastly, we describe the recent efforts to apply systems biology approaches to dissect the role of lipid mediators during bacterial and viral infections in vivo.
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Affiliation(s)
- Vincent C Tam
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA.
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28
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Norris PC, Dennis EA. A lipidomic perspective on inflammatory macrophage eicosanoid signaling. Adv Biol Regul 2013; 54:99-110. [PMID: 24113376 DOI: 10.1016/j.jbior.2013.09.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 09/15/2013] [Accepted: 09/17/2013] [Indexed: 12/24/2022]
Abstract
Macrophages are central to essential physiological processes including the regulation of innate and adaptive immunity, but they are also central to a number of inflammatory disease states. These immune cells also possess remarkable plasticity and display various shades of functionalities based on changes in the surrounding molecular environment. Macrophage biology has defined various phenotypes and roles in inflammation based primarily on cytokine and chemokine profiles of cells in different activation states. Importantly, macrophages are elite producers of eicosanoids and other related lipid mediators during inflammation, but specific roles of these molecules have not generally been incorporated into the larger context of macrophage biology. In this review, we discuss the current classification of macrophage types and their roles in inflammation and disease, along with the practical challenges of studying biologically relevant phenotypes ex vivo. Using the latest advances in eicosanoid lipidomics, we highlight several key studies from our laboratory that provide a comprehensive understanding of how eicosanoid metabolism differs between macrophage phenotypes, along with how this metabolism is altered by changes in membrane fatty acid distribution and varied durations of Toll-like receptor (TLR) priming. In conclusion, we summarize several examples of the benefit of macrophage plasticity to develop accurate cellular mechanisms of lipid metabolism, and insights from lipidomic analyses about the differences in eicosanoid pathway enzyme activity in vitro vs. in cells ex vivo. Examples of new techniques to further understand the role of macrophage eicosanoid signaling in vivo are also discussed.
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Affiliation(s)
- Paul C Norris
- Departments of Chemistry/Biochemistry and Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0601, USA
| | - Edward A Dennis
- Departments of Chemistry/Biochemistry and Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0601, USA.
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29
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Abstract
The lipidome is composed of all of the biomolecules defined as lipids, which encompass compounds of amazing structural diversity and complexity. It has been ∼1 decade since the study of "lipidomics" was begun in earnest, and the technologies and tools for data analysis have advanced considerably over this period. This workshop summarized the scope of the lipidome and technologies for its analysis, lipidomics databases and other online tools, and examples of the application of lipidomics to nutritional research. The slides from the workshop, online lipidomics tools, and databases are available at http://www.lipidmaps.org.
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Affiliation(s)
| | - Edward A. Dennis
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, CA
| | - Jeffrey G. McDonald
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eoin Fahy
- San Diego Supercomputing Center, University of California, San Diego, CA
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Abstract
Abstract Metabolomics technologies enable the examination and identification of endogenous biochemical reaction products, revealing information on the precise metabolic pathways and processes within a living cell. Metabolism is either directly or indirectly involved with every aspect of cell function, and metabolomics is thus believed to be a reflection of the phenotype of any cell. Metabolomics analysis of cells has many potential applications and advantages compared to currently used methods in the postgenomics era. Cell metabolomics is an emerging field that addresses fundamental biological questions and allows one to observe metabolic phenomena in cells. Cell metabolomics consists of four sequential steps: (a) sample preparation and extraction, (b) metabolic profiles of low-weight metabolites based on MS or NMR spectroscopy techniques, (c) pattern recognition approaches and bioinformatics data analysis, (d) metabolites identification resulting in putative biomarkers and molecular targets. The biomarkers are eventually placed in metabolic networks to provide insight on the cellular biochemical phenomena. This article analyzes the recent developments in use of metabolomics to characterize and interpret the cellular metabolome in a wide range of pathophysiological and clinical contexts, and the putative roles of the endogenous small molecule metabolites in this new frontier of postgenomics biology and systems medicine.
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Affiliation(s)
- Aihua Zhang
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Chinmedomics, Key Pharmacometabolomics Platform of Chinese Medicines, and Heilongjiang University of Chinese Medicine , Harbin, China
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31
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Dinasarapu AR, Gupta S, Ram Maurya M, Fahy E, Min J, Sud M, Gersten MJ, Glass CK, Subramaniam S. A combined omics study on activated macrophages--enhanced role of STATs in apoptosis, immunity and lipid metabolism. Bioinformatics 2013; 29:2735-43. [PMID: 23981351 DOI: 10.1093/bioinformatics/btt469] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Macrophage activation by lipopolysaccharide and adenosine triphosphate (ATP) has been studied extensively because this model system mimics the physiological context of bacterial infection and subsequent inflammatory responses. Previous studies on macrophages elucidated the biological roles of caspase-1 in post-translational activation of interleukin-1β and interleukin-18 in inflammation and apoptosis. However, the results from these studies focused only on a small number of factors. To better understand the host response, we have performed a high-throughput study of Kdo2-lipid A (KLA)-primed macrophages stimulated with ATP. RESULTS The study suggests that treating mouse bone marrow-derived macrophages with KLA and ATP produces 'synergistic' effects that are not seen with treatment of KLA or ATP alone. The synergistic regulation of genes related to immunity, apoptosis and lipid metabolism is observed in a time-dependent manner. The synergistic effects are produced by nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) and activator protein (AP)-1 through regulation of their target cytokines. The synergistically regulated cytokines then activate signal transducer and activator of transcription (STAT) factors that result in enhanced immunity, apoptosis and lipid metabolism; STAT1 enhances immunity by promoting anti-microbial factors; and STAT3 contributes to downregulation of cell cycle and upregulation of apoptosis. STAT1 and STAT3 also regulate glycerolipid and eicosanoid metabolism, respectively. Further, western blot analysis for STAT1 and STAT3 showed that the changes in transcriptomic levels were consistent with their proteomic levels. In summary, this study shows the synergistic interaction between the toll-like receptor and purinergic receptor signaling during macrophage activation on bacterial infection. AVAILABILITY Time-course data of transcriptomics and lipidomics can be queried or downloaded from http://www.lipidmaps.org. CONTACT shankar@ucsd.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ashok Reddy Dinasarapu
- Department of Bioengineering, San Diego Super Computer Center, Department of Cellular and Molecular Medicine and Department of Chemistry and Biochemistry, University of California San Diego, CA 92093, USA
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32
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Sabidó E, Wu Y, Bautista L, Porstmann T, Chang CY, Vitek O, Stoffel M, Aebersold R. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Mol Syst Biol 2013; 9:681. [PMID: 23860498 PMCID: PMC3734509 DOI: 10.1038/msb.2013.36] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 06/01/2013] [Indexed: 12/16/2022] Open
Abstract
Quantitative measurement of proteins involved in insulin signaling and central metabolism in C57BL/6J and 129Sv mice subjected to a sustained high-fat diet reveals that the two strains diverge early in their response to the feeding regimen. ![]()
Quantitative targeted protein measurements were designed to quantify murine proteins covering the insulin-signaling pathway
and the lipid and carbohydrate metabolism and used to compare the differential effect of a persistent high-fat diet in C57BL/6J
and 129Sv mouse strains. Differential effect of a persistent high-fat diet were compared in C57BL/6J and 129Sv mouse strains. Differences in protein abundances suggest that peroxisomal β-oxidation is actively promoted in fatty C57BL/6J mice whereas
lipogenesis activation dominates the response of 129Sv mice. Most strain-specific changes were apparent early in the regimen when phenotypic changes were already set, but not yet very
pronounced and they allow a clear discrimination of the mouse strains at an early stage during the long-term high-fat diet. Persistent high-fat diet also alters the transient changes that normally occur in C57BL/6J and 129Sv mice in response to fasting
or food intake.
The metabolic syndrome is a collection of risk factors including obesity, insulin resistance and hepatic steatosis, which occur together and increase the risk of diseases such as diabetes, cardiovascular disease and cancer. In spite of intense research, the complex etiology of insulin resistance and its association with the accumulation of triacylglycerides in the liver and with hepatic steatosis remains not completely understood. Here, we performed quantitative measurements of 144 proteins involved in the insulin-signaling pathway and central metabolism in liver homogenates of two genetically well-defined mouse strains C57BL/6J and 129Sv that were subjected to a sustained high-fat diet. We used targeted mass spectrometry by selected reaction monitoring (SRM) to generate accurate and reproducible quantitation of the targeted proteins across 36 different samples (12 conditions and 3 biological replicates), generating one of the largest quantitative targeted proteomics data sets in mammalian tissues. Our results revealed rapid response to high-fat diet that diverged early in the feeding regimen, and evidenced a response to high-fat diet dominated by the activation of peroxisomal β-oxidation in C57BL/6J and by lipogenesis in 129Sv mice.
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Affiliation(s)
- Eduard Sabidó
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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33
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Maurya MR, Gupta S, Li X, Fahy E, Dinasarapu AR, Sud M, Brown HA, Glass CK, Murphy RC, Russell DW, Dennis EA, Subramaniam S. Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages. J Lipid Res 2013; 54:2525-42. [PMID: 23776196 DOI: 10.1194/jlr.m040212] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies of macrophage biology have been significantly advanced by the availability of cell lines such as RAW264.7 cells. However, it is unclear how these cell lines differ from primary macrophages such as thioglycolate-elicited peritoneal macrophages (TGEMs). We used the inflammatory stimulus Kdo2-lipid A (KLA) to stimulate RAW264.7 and TGEM cells. Temporal changes of lipid and gene expression levels were concomitantly measured and a systems-level analysis was performed on the fold-change data. Here we present a comprehensive comparison between the two cell types. Upon KLA treatment, both RAW264.7 and TGEM cells show a strong inflammatory response. TGEM (primary) cells show a more rapid and intense inflammatory response relative to RAW264.7 cells. DNA levels (fold-change relative to control) are reduced in RAW264.7 cells, correlating with greater downregulation of cell cycle genes. The transcriptional response suggests that the cholesterol de novo synthesis increases considerably in RAW264.7 cells, but 25-hydroxycholesterol increases considerably in TGEM cells. Overall, while RAW264.7 cells behave similarly to TGEM cells in some ways and can be used as a good model for inflammation- and immune function-related kinetic studies, they behave differently than TGEM cells in other aspects of lipid metabolism and phenotypes used as models for various disorders such as atherosclerosis.
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Affiliation(s)
- Mano R Maurya
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
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34
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Kanter JE, Bornfeldt KE. Inflammation and diabetes-accelerated atherosclerosis: myeloid cell mediators. Trends Endocrinol Metab 2013; 24:137-44. [PMID: 23153419 PMCID: PMC3578033 DOI: 10.1016/j.tem.2012.10.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 12/29/2022]
Abstract
Monocytes and macrophages respond to and govern inflammation by producing a plethora of inflammatory modulators, including cytokines, chemokines, and arachidonic acid (C20:4)-derived lipid mediators. One of the most prevalent inflammatory diseases is cardiovascular disease, caused by atherosclerosis, and accelerated by diabetes. Recent research has demonstrated that monocytes/macrophages from diabetic mice and humans with type 1 diabetes show upregulation of the enzyme, acyl-CoA synthetase 1 (ACSL1), which promotes C20:4 metabolism, and that ACSL1 inhibition selectively protects these cells from the inflammatory and proatherosclerotic effects of diabetes, in mice. Increased understanding of the role of ACSL1 and other culprits in monocytes/macrophages in inflammation and diabetes-accelerated atherosclerosis offers hope for new treatment strategies to combat diabetic vascular disease.
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Affiliation(s)
- Jenny E Kanter
- Department of Medicine, Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, WA 98109, USA
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35
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Abstract
Chronic persistent inflammation plays a significant role in disease pathology of cancer, cardiovascular disease, and metabolic syndrome (MetS). MetS is a constellation of diseases that include obesity, diabetes, hypertension, dyslipidemia, hypertriglyceridemia, and hypercholesterolemia. Nonalcoholic fatty liver disease (NAFLD) is associated with many of the MetS diseases. These metabolic derangements trigger a persistent inflammatory cascade, which includes production of lipid autacoids (eicosanoids) that recruit immune cells to the site of injury and subsequent expression of cytokines and chemokines that amplify the inflammatory response. In acute inflammation, the transcellular synthesis of antiinflammatory eicosanoids resolve inflammation, while persistent activation of the autacoid-cytokine-chemokine cascade in metabolic disease leads to chronic inflammation and accompanying tissue pathology. Many drugs targeting the eicosanoid pathways have been shown to be effective in the treatment of MetS, suggesting a common linkage between inflammation, MetS and drug metabolism. The cross-talk between inflammation and MetS seems apparent because of the growing evidence linking immune cell activation and metabolic disorders such as insulin resistance, dyslipidemia, and hypertriglyceridemia. Thus modulation of lipid metabolism through either dietary adjustment or selective drugs may become a new paradigm in the treatment of metabolic disorders. This review focuses on the mechanisms linking eicosanoid metabolism to persistent inflammation and altered lipid and carbohydrate metabolism in MetS.
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Affiliation(s)
- James P Hardwick
- Biochemistry and Molecular Pathology, Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA.
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