151
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Frediani JK, Jones DP, Tukvadze N, Uppal K, Sanikidze E, Kipiani M, Tran VT, Hebbar G, Walker DI, Kempker RR, Kurani SS, Colas RA, Dalli J, Tangpricha V, Serhan CN, Blumberg HM, Ziegler TR. Plasma metabolomics in human pulmonary tuberculosis disease: a pilot study. PLoS One 2014; 9:e108854. [PMID: 25329995 PMCID: PMC4198093 DOI: 10.1371/journal.pone.0108854] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/26/2014] [Indexed: 12/31/2022] Open
Abstract
We aimed to characterize metabolites during tuberculosis (TB) disease and identify new pathophysiologic pathways involved in infection as well as biomarkers of TB onset, progression and resolution. Such data may inform development of new anti-tuberculosis drugs. Plasma samples from adults with newly diagnosed pulmonary TB disease and their matched, asymptomatic, sputum culture-negative household contacts were analyzed using liquid chromatography high-resolution mass spectrometry (LC-MS) to identify metabolites. Statistical and bioinformatics methods were used to select accurate mass/charge (m/z) ions that were significantly different between the two groups at a false discovery rate (FDR) of q<0.05. Two-way hierarchical cluster analysis (HCA) was used to identify clusters of ions contributing to separation of cases and controls, and metabolomics databases were used to match these ions to known metabolites. Identity of specific D-series resolvins, glutamate and Mycobacterium tuberculosis (Mtb)-derived trehalose-6-mycolate was confirmed using LC-MS/MS analysis. Over 23,000 metabolites were detected in untargeted metabolomic analysis and 61 metabolites were significantly different between the two groups. HCA revealed 8 metabolite clusters containing metabolites largely upregulated in patients with TB disease, including anti-TB drugs, glutamate, choline derivatives, Mycobacterium tuberculosis-derived cell wall glycolipids (trehalose-6-mycolate and phosphatidylinositol) and pro-resolving lipid mediators of inflammation, known to stimulate resolution, efferocytosis and microbial killing. The resolvins were confirmed to be RvD1, aspirin-triggered RvD1, and RvD2. This study shows that high-resolution metabolomic analysis can differentiate patients with active TB disease from their asymptomatic household contacts. Specific metabolites upregulated in the plasma of patients with active TB disease, including Mtb-derived glycolipids and resolvins, have potential as biomarkers and may reveal pathways involved in TB disease pathogenesis and resolution.
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Affiliation(s)
- Jennifer K. Frediani
- Nutrition and Health Sciences, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, United States of America
- Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Dean P. Jones
- Nutrition and Health Sciences, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, United States of America
- Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (TRZ); (DPJ)
| | - Nestan Tukvadze
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - Karan Uppal
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Eka Sanikidze
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - Maia Kipiani
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - ViLinh T. Tran
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Gautam Hebbar
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Douglas I. Walker
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts, United States of America
| | - Russell R. Kempker
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Shaheen S. Kurani
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Romain A. Colas
- Center for Experimental Therapeutics and Reperfusion Injury, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jesmond Dalli
- Center for Experimental Therapeutics and Reperfusion Injury, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vin Tangpricha
- Nutrition and Health Sciences, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, United States of America
- Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Atlanta Veterans Affairs Medical Center, Decatur, Georgia, United States of America
| | - Charles N. Serhan
- Center for Experimental Therapeutics and Reperfusion Injury, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Henry M. Blumberg
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Thomas R. Ziegler
- Nutrition and Health Sciences, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, United States of America
- Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (TRZ); (DPJ)
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152
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Zhu X, Lei H, Wu J, Li JV, Tang H, Wang Y. Systemic responses of BALB/c mice to Salmonella typhimurium infection. J Proteome Res 2014; 13:4436-45. [PMID: 25209111 DOI: 10.1021/pr500770x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Salmonella typhimurium is a bacterial pathogen that poses a great threat to humans and animals. In order to discover hosts' responses to S. typhimurium infection, we collected and analyzed biofluids and organ tissues from mice which had ingested S. typhimurium. We employed (1)H NMR spectroscopy coupled with multivariate data analysis and immunological techniques. The results indicate that infection leads to a severe impact on mice spleen and ileum, which are characterized by splenomegaly and edematous villi, respectively. We found that increased levels of itaconic acid were correlated with the presence of splenomegaly during infection and may play an important role in Salmonella-containing vacuole acidification. In addition, metabonomic analyses of urine displayed the development of salmonellosis in mice, which is characterized by dynamic changes in energy metabolism. Furthermore, we found that the presence of S. typhimurium activated an anti-oxidative response in infected mice. We also observed changes in the gut microbial co-metabolites (hippurate, TMAO, TMA, methylamine). This investigation sheds much needed light on the host-pathogen interactions of S. typhimurium, providing further information to deepen our understanding of the long co-evolution process between hosts and infective bacteria.
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Affiliation(s)
- Xiaoyang Zhu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
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153
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Abstract
Several major pathogens, including Mycobacterium tuberculosis, parasitize host cells and exploit host-derived nutrients to sustain their own metabolism. Although the carbon sources that are used by M. tuberculosis have been extensively studied, the mechanisms by which mycobacteria capture and metabolize nitrogen, which is another essential constituent of biomolecules, have only recently been revisited. In this Progress article, we discuss central nitrogen metabolism in M. tuberculosis, the mechanisms that are used by this pathogen to obtain nitrogen from its host and the potential role of nitrogen capture and metabolism in virulence.
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154
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Metabolomics: a window into the adaptive physiology of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2014; 94:538-43. [PMID: 25172023 DOI: 10.1016/j.tube.2014.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB) and second leading cause of human mortality due to a single infectious agent. This is mostly because of M. tuberculosis' ability to adapt its metabolism to the host environment and regulate entry into and exit from cell cycle. Knowledge of the specific metabolic changes accompanying these transitions however is incomplete. Metabolomics has emerged as a new biochemical window into M. tuberculosis physiology. This review highlights recent insights from the application of such technologies to studies of the M. tuberculosis lifecycle.
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155
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Bacterial itaconate degradation promotes pathogenicity. Nat Chem Biol 2014; 10:371-7. [PMID: 24657929 DOI: 10.1038/nchembio.1482] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/14/2014] [Indexed: 12/30/2022]
Abstract
Itaconate (methylenesuccinate) was recently identified as a mammalian metabolite whose production is substantially induced during macrophage activation. This compound is a potent inhibitor of isocitrate lyase, a key enzyme of the glyoxylate cycle, which is a pathway required for the survival of many pathogens inside the eukaryotic host. Here we show that numerous bacteria, notably many pathogens such as Yersinia pestis and Pseudomonas aeruginosa, have three genes for itaconate degradation. They encode itaconate coenzyme A (CoA) transferase, itaconyl-CoA hydratase and (S)-citramalyl-CoA lyase, formerly referred to as CitE-like protein. These genes are known to be crucial for survival of some pathogens in macrophages. The corresponding enzymes convert itaconate into the cellular building blocks pyruvate and acetyl-CoA, thus enabling the bacteria to metabolize itaconate and survive in macrophages. The itaconate degradation and detoxification pathways of Yersinia and Pseudomonas are the result of convergent evolution. This work revealed a common persistence factor operating in many pathogenic bacteria.
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156
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1H NMR-based metabolite profiling of plasma in a rat model of chronic kidney disease. PLoS One 2014; 9:e85445. [PMID: 24465563 PMCID: PMC3896356 DOI: 10.1371/journal.pone.0085445] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 11/28/2013] [Indexed: 12/21/2022] Open
Abstract
Chronic kidney disease (CKD) is characterized by the gradual loss of the kidney function to excrete wastes and fluids from the blood. 1H NMR-based metabolomics was exploited to investigate the altered metabolic pattern in rats with CKD induced by surgical reduction of the renal mass (i.e., 5/6 nephrectomy (5/6 Nx)), particularly for identifying specific metabolic biomarkers associated with early of CKD. Plasma metabolite profiling was performed in CKD rats (at 4- or 8-weeks after 5/6 Nx) compared to sham-operated rats. Principle components analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) score plots showed a significant separation between the groups. The resulting metabolic profiles demonstrated significantly increased plasma levels of organic anions, including citrate, β-hydroxybutyrate, lactate, acetate, acetoacetate, and formate in CKD. Moreover, levels of alanine, glutamine, and glutamate were significantly higher. These changes were likely to be associated with complicated metabolic acidosis in CKD for counteracting systemic metabolic acidosis or increased protein catabolism from muscle. In contrast, levels of VLDL/LDL (CH2)n and N-acetylglycoproteins were decreased. Taken together, the observed changes of plasma metabolite profiles in CKD rats provide insights into the disturbed metabolism in early phase of CKD, in particular for the altered metabolism of acid-base and/or amino acids.
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157
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Whitworth HS, Aranday-Cortes E, Lalvani A. Biomarkers of tuberculosis: a research roadmap. Biomark Med 2013; 7:349-62. [PMID: 23734796 DOI: 10.2217/bmm.13.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) continues to represent a major public health problem worldwide. Prompt and accurate diagnosis and effective treatment are fundamental to reducing morbidity and mortality and curtailing spread of infection. Furthermore, tackling the large reservoir of latent infection is the cornerstone to TB control in many high income low TB incidence countries. However, our existing toolkit for prevention, diagnosis and treatment remains outdated and inadequate. Here, we discuss the key targets for biomarker research and discovery in TB and recent developments in the field. We focus on host biomarkers, in particular: correlates of vaccine efficacy and sterilizing immunity; biomarkers of latent TB infection, including diagnosis, risk of progression to active TB and response to treatment; and markers of active TB, including diagnosis, response to treatment and risk of relapse. Recent scientific and technological advances have contributed to significant recent progression in biomarker discovery. Although there are clear remaining paucities, continued efforts within scientific, translational and clinical studies are likely to yield a number of clinically useful biomarkers of TB in the foreseeable future.
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Affiliation(s)
- Hilary S Whitworth
- Tuberculosis Research Unit, Department of Respiratory Medicine, National Heart & Lung Institute, Imperial College London, London W2 1PG, UK
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158
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Chen Y, Wu J, Tu L, Xiong X, Hu X, Huang J, Xu Z, Zhang X, Hu C, Hu X, Guo A, Wang Y, Chen H. (1)H-NMR spectroscopy revealed Mycobacterium tuberculosis caused abnormal serum metabolic profile of cattle. PLoS One 2013; 8:e74507. [PMID: 24098654 PMCID: PMC3787013 DOI: 10.1371/journal.pone.0074507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/02/2013] [Indexed: 01/17/2023] Open
Abstract
To re-evaluate virulence of Mycobacterium tuberculosis (M. tb) in cattle, we experimentally infected calves with M. tb andMycobacterium bovisvia intratracheal injection at a dose of 2.0×107 CFU and observed the animals for 33 weeks. The intradermal tuberculin test and IFN-γin vitro release assay showed that both M. tb and M. bovis induced similar responses. Immunohistochemical staining of pulmonary lymph nodes indicated that the antigen MPB83 of both M. tb and M. bovis were similarly distributed in the tissue samples. Histological examinations showed all of the infected groups exhibited neutrophil infiltration to similar extents. Although the infected cattle did not develop granulomatous inflammation, the metabolic profiles changed significantly, which were characterized by a change in energy production pathways and increased concentrations of N-acetyl glycoproteins. Glycolysis was induced in the infected cattle by decreased glucose and increased lactate content, and enhanced fatty acid β-oxidation was induced by decreased TG content, and decreased gluconeogenesis indicated by the decreased concentration of glucogenic and ketogenic amino acids promoted utilization of substances other than glucose as energy sources. In addition, an increase in acute phase reactive serum glycoproteins, together with neutrophil infiltration and increased of IL-1β production indicated an early inflammatory response before granuloma formation. In conclusion, this study indicated that both M. tb and M.bovis were virulent to cattle. Therefore, it is likely that cattle with M. tb infections would be critical to tuberculosis transmission from cattle to humans. Nuclear magnetic resonance was demonstrated to be an efficient method to systematically evaluate M. tb and M. bovi sinfection in cattle.
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Affiliation(s)
- Yingyu Chen
- The National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Junfang Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Lingling Tu
- The National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Wuhan Keqian Animal Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Xuekai Xiong
- The National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xidan Hu
- Xinjiang Academy of Animal Husbandry and Veterinary Institute, Urumqi, Xinjiang, China
| | - Jiong Huang
- Xinjiang Academy of Animal Husbandry and Veterinary Institute, Urumqi, Xinjiang, China
| | - Zhiguang Xu
- Xinjiang Academy of Animal Husbandry and Veterinary Institute, Urumqi, Xinjiang, China
| | - Xiansong Zhang
- The National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xueying Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Aizhen Guo
- The National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail: (AG); (YW)
| | - Yulan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail: (AG); (YW)
| | - Huanchun Chen
- The National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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159
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Zhou A, Ni J, Xu Z, Wang Y, Lu S, Sha W, Karakousis PC, Yao YF. Application of (1)h NMR spectroscopy-based metabolomics to sera of tuberculosis patients. J Proteome Res 2013; 12:4642-9. [PMID: 23980697 DOI: 10.1021/pr4007359] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an ideal platform for the metabolic analysis of biofluids due to its high reproducibility, nondestructiveness, nonselectivity in metabolite detection, and the ability to simultaneously quantify multiple classes of metabolites. Tuberculosis (TB) is a chronic wasting inflammatory disease characterized by multisystem involvement, which can cause metabolic derangements in afflicted patients. In this study, we combined multivariate pattern recognition (PR) analytical techniques with (1)H NMR spectroscopy to explore the metabolic profile of sera from TB patients. A total of 77 serum samples obtained from patients with TB (n = 38) and healthy controls (n = 39) were investigated. Orthogonal partial least-squares discriminant analysis (OPLS-DA) was capable of distinguishing TB patients from controls and establishing a TB-specific metabolite profile. A total of 17 metabolites differed significantly in concentration between the two groups. Serum samples from TB patients were characterized by increased concentrations of 1-methylhistidine, acetoacetate, acetone, glutamate, glutamine, isoleucine, lactate, lysine, nicotinate, phenylalanine, pyruvate, and tyrosine, accompanied by reduced concentrations of alanine, formate, glycine, glycerolphosphocholine, and low-density lipoproteins relative to control subjects. Our study reveals the metabolic profile of sera from TB patients and indicates that NMR-based methods can distinguish TB patients from healthy controls. NMR-based metabolomics has the potential to be developed into a novel clinical tool for TB diagnosis or therapeutic monitoring and could contribute to an improved understanding of disease mechanisms.
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Affiliation(s)
- Aiping Zhou
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine , 280 South Chongqing Road, Shanghai 200025, China
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160
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Jung J, Kim SH, Lee HS, Choi GS, Jung YS, Ryu DH, Park HS, Hwang GS. Serum metabolomics reveals pathways and biomarkers associated with asthma pathogenesis. Clin Exp Allergy 2013; 43:425-33. [PMID: 23517038 DOI: 10.1111/cea.12089] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND Asthma is a chronic inflammatory disease caused by complex interactions of genetic, epigenetic, and environmental factors. For this reason, new approaches are required to clarify the pathogenesis of asthma by systemic review. OBJECTIVE We applied a (1)H-NMR metabolomics approach to investigate the altered metabolic pattern in sera from patients with asthma and sought to identify the mechanism underlying asthma and potential biomarkers. METHOD A global profile of sera from patients with asthma (n = 39) and controls (n = 26) was generated using (1)H-NMR spectroscopy coupled with multivariate statistical analysis. Endogenous metabolites in serum were rapidly measured using the target-profiling procedure. RESULTS Multivariate statistical analysis showed a clear distinction between patients with asthma and healthy subjects. Sera of asthma patients were characterized by increased levels of methionine, glutamine, and histidine and by decreased levels of formate, methanol, acetate, choline, O-phosphocholine, arginine, and glucose. The metabolites detected in the sera of patients with asthma are involved in hypermethylation, response to hypoxia, and immune reaction. Furthermore, the levels of serum metabolites from patients with asthma correlated with asthma severity; in particular, lipid metabolism was altered in patients with lower forced expiratory volume in 1 s percentage (FEV(1)%) predicted values. In addition, potential biomarkers showed strong predictive power in ROC analysis, and the presence of asthma in external validation models was predicted with high accuracy (90.9% for asthma and 100% for control subjects). CONCLUSION & CLINICAL RELEVANCE These data showed that (1)H-NMR-based metabolite profiling of serum may be useful for the effective diagnosis of asthma and a further understanding of its pathogenesis.
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Affiliation(s)
- J Jung
- Integrated Metabolomics Research Group, Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
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161
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Ghosh S, Sengupta A, Sharma S, Sonawat HM. Metabolic perturbations of kidney and spleen in murine cerebral malaria: (1)H NMR-based metabolomic study. PLoS One 2013; 8:e73113. [PMID: 24039868 PMCID: PMC3765208 DOI: 10.1371/journal.pone.0073113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/18/2013] [Indexed: 02/02/2023] Open
Abstract
A significant fraction of global population is under the threat of malaria. Majority of annual death is due to the more complicated form of the infection i.e. the cerebral form, also known as Cerebral Malaria (CM). Host parasite interaction is known to cause a cascade of events in various tissues like brain, liver, kidney, and spleen. We have employed (1)H NMR based metabolomics to understand the specific perturbations of various tissues in CM. In our previous paper we have delineated the differences between CM vis-a-vis non-cerebral malaria (NCM) mice in serum, liver and brain. In this paper we focus on their differences of metabolic profile in kidney and spleen as kidney dysfunction and splenomegaly are known to be associated to neurological outcome of the disease. Moreover we have also looked into how the biological compartments (kidney, spleen and serum) interact with each other. The various metabolites involved in such interactions and their correlational aspects across the compartments have been studied in CM, NCM and control mice. The idea was to find out the specific pathways that are altered in CM mice. Our results demonstrate that both the kidney as well as spleen metabolism are differentially perturbed in CM with respect to NCM. The results point out that glutamate levels are decreased in CM mice with respect to NCM mice both in case of spleen and kidney while creatine, myo-inositol and betaine levels are increased in kidney of CM mice with respect to NCM mice. From the analysis of Multiway Principal Component Analysis (MPCA) we see that lipid metabolism and TCA cycle is altered in kidney and spleen.
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Affiliation(s)
- Soumita Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Arjun Sengupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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162
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Decreased serum 5-oxoproline in TB patients is associated with pathological damage of the lung. Clin Chim Acta 2013; 423:5-9. [DOI: 10.1016/j.cca.2013.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/08/2013] [Accepted: 04/11/2013] [Indexed: 11/19/2022]
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163
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Eisenreich W, Heesemann J, Rudel T, Goebel W. Metabolic host responses to infection by intracellular bacterial pathogens. Front Cell Infect Microbiol 2013; 3:24. [PMID: 23847769 PMCID: PMC3705551 DOI: 10.3389/fcimb.2013.00024] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/11/2013] [Indexed: 12/12/2022] Open
Abstract
The interaction of bacterial pathogens with mammalian hosts leads to a variety of physiological responses of the interacting partners aimed at an adaptation to the new situation. These responses include multiple metabolic changes in the affected host cells which are most obvious when the pathogen replicates within host cells as in case of intracellular bacterial pathogens. While the pathogen tries to deprive nutrients from the host cell, the host cell in return takes various metabolic countermeasures against the nutrient theft. During this conflicting interaction, the pathogen triggers metabolic host cell responses by means of common cell envelope components and specific virulence-associated factors. These host reactions generally promote replication of the pathogen. There is growing evidence that pathogen-specific factors may interfere in different ways with the complex regulatory network that controls the carbon and nitrogen metabolism of mammalian cells. The host cell defense answers include general metabolic reactions, like the generation of oxygen- and/or nitrogen-reactive species, and more specific measures aimed to prevent access to essential nutrients for the respective pathogen. Accurate results on metabolic host cell responses are often hampered by the use of cancer cell lines that already exhibit various de-regulated reactions in the primary carbon metabolism. Hence, there is an urgent need for cellular models that more closely reflect the in vivo infection conditions. The exact knowledge of the metabolic host cell responses may provide new interesting concepts for antibacterial therapies.
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Affiliation(s)
- Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Technische Universität München Garching, Germany
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164
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Zhang F, Wang D, Li X, Li Z, Chao J, Qin X. Metabolomic study of the fever model induced by baker's yeast and the antipyretic effects of aspirin in rats using nuclear magnetic resonance and gas chromatography-mass spectrometry. J Pharm Biomed Anal 2013; 81-82:168-77. [PMID: 23670098 DOI: 10.1016/j.jpba.2013.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/01/2013] [Accepted: 04/06/2013] [Indexed: 11/28/2022]
Abstract
A metabolomic investigation of baker's yeast-induced fever in rats was carried out. Plasma derived from Sprague-Dawley rats treated by subcutaneous administration of 20% (w/v) baker's yeast was analyzed using gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR). Statistical data analysis using t-test and orthogonal partial least-squares discriminant analysis revealed many significant changes in the metabolic data in the plasma of the fever group. Clear separation was achieved between the fever and control groups. Seventeen marked metabolites were found in the fever group. The metabolites, which include amino acids, carbohydrate, organic acids, and fatty acids, mostly contributed to the discrimination of plasma samples from the control and fever groups. These results suggested that fever may involve in the perturbation of amino acid metabolism coupled with energy metabolism, lipid metabolism, and glycometabolism. After determining the antipyretic effects of aspirin on the fever group, four metabolites in the fever rat plasma were found to be signally regulated and recognized as potential biomarkers, including 3-hydroxybutyric acid, gamma-aminobutyric acid, glucose, and linoleic acid. The metabolic relationships that possibly exist between these potential biomarkers were speculated, and the mechanism of baker's yeast-induced fever was illustrated based on the metabolic relationships. This study found that metabolomic approaches such as GC-MS and NMR could be used as potential powerful tools to investigate the biochemical changes and mechanisms in certain pathological states at the metabolism level.
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Affiliation(s)
- Fusheng Zhang
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, No. 92, Wucheng Road, Taiyuan 030006, Shanxi, PR China
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165
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(1)H NMR-based metabolite profiling of planktonic and biofilm cells in Acinetobacter baumannii 1656-2. PLoS One 2013; 8:e57730. [PMID: 23483923 PMCID: PMC3590295 DOI: 10.1371/journal.pone.0057730] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/25/2013] [Indexed: 01/21/2023] Open
Abstract
Acinetobacter baumannii is an aerobic and gram-negative pathogenic bacterium that is resistant to most antibiotics. Recently, A. baumannii 1656-2 exhibited the ability to form biofilms under clinical conditions. In this study, global metabolite profiling of both planktonic and biofilm forms of A. baumannii 1656-2 was performed using high-resolution nuclear magnetic resonance (NMR) spectroscopy and multivariate statistical analysis to investigate the metabolic patterns leading to biofilm formation. Principal components analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) score plots showed a distinct separation between planktonic and biofilm cells. Metabolites including acetates, pyruvate, succinate, UDP-glucose, AMP, glutamate, and lysine were increasingly involved in the energy metabolism of biofilm formation. In particular, the ratio of N-acetyl-D-glucosamine (GlcNAc) to D-glucosamine (GlcNH2) was significantly higher during biofilm formation than under the planktonic condition. This study demonstrates that NMR-based global metabolite profiling of bacterial cells can provide valuable insight into the metabolic changes in multidrug resistant and biofilm-forming bacteria such as A. baumannii 1656-2.
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166
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Benahmed MA, Elbayed K, Daubeuf F, Santelmo N, Frossard N, Namer IJ. NMR HRMAS spectroscopy of lung biopsy samples: Comparison study between human, pig, rat, and mouse metabolomics. Magn Reson Med 2013; 71:35-43. [PMID: 23412987 DOI: 10.1002/mrm.24658] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 01/03/2013] [Accepted: 01/03/2013] [Indexed: 11/07/2022]
Abstract
PURPOSE Using the metabolomics by NMR high-resolution magic angle spinning spectroscopy, we assessed the lung metabolome of various animal species in order to identify the animal model that could be substituted to human lung in studies on fresh lung biopsies. METHODS The experiments were conducted on intact lung biopsy samples of pig, rat, mouse, and human using a Bruker Advance III 500 spectrometer. Thirty-five to 39 metabolites were identified and 23 metabolites were quantified. Principal component analysis, partial least-squares discriminant analysis, and analysis of variance tests were performed in order to compare the metabolic profiles of each animal lung biopsies to those of the human lung. RESULTS The metabolic composition between human and pig lung was similar. However, human lung was distinguishable from mouse and rat regarding: Trimethylamine N-oxide and betaïne which were present in rodents but not in human lung, carnitine, and glycerophosphocholine which were present in mouse but not in human lung. Conversely, succinic acid was undetected in rat lung. Furthermore, fatty acids concentration was significantly higher in rodent lungs compared to human lung. CONCLUSION Using the metabolomics by NMR high-resolution magic angle spinning spectroscopy on lung biopsy, samples allowed to highlight that pig lung seems to be close to human lung as regarding its metabolite composition with more similarities than dissimilarities.
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Affiliation(s)
- Malika A Benahmed
- Faculté de Médecine, Laboratoire d'Imagerie et de Neurosciences Cognitives (LINC), Institut de Physique Biologique, Université de Strasbourg/CNRS UMR7237, Strasbourg Cedex, France; Laboratoire de RMN et Biophysique des membranes, Institut de Chimie, Université de Strasbourg/CNRS UMR7177, Strasbourg, France
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167
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Phong WY, Lin W, Rao SPS, Dick T, Alonso S, Pethe K. Characterization of phosphofructokinase activity in Mycobacterium tuberculosis reveals that a functional glycolytic carbon flow is necessary to limit the accumulation of toxic metabolic intermediates under hypoxia. PLoS One 2013; 8:e56037. [PMID: 23409118 PMCID: PMC3567006 DOI: 10.1371/journal.pone.0056037] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 01/04/2013] [Indexed: 11/18/2022] Open
Abstract
Metabolic versatility has been increasingly recognized as a major virulence mechanism that enables Mycobacterium tuberculosis to persist in many microenvironments encountered in its host. Glucose is one of the most abundant carbon sources that is exploited by many pathogenic bacteria in the human host. M. tuberculosis has an intact glycolytic pathway that is highly conserved in all clinical isolates sequenced to date suggesting that glucose may represent a non-negligible source of carbon and energy for this pathogen in vivo. Fructose-6-phosphate phosphorylation represents the key-committing step in glycolysis and is catalyzed by a phosphofructokinase (PFK) activity. Two genes, pfkA and pfkB have been annotated to encode putative PFK in M. tuberculosis. Here, we show that PFKA is the sole PFK enzyme in M. tuberculosis with no functional redundancy with PFKB. PFKA is required for growth on glucose as sole carbon source. In co-metabolism experiments, we report that disruption of the glycolytic pathway at the PFK step results in intracellular accumulation of sugar-phosphates that correlated with significant impairment of the cell viability. Concomitantly, we found that the presence of glucose is highly toxic for the long-term survival of hypoxic non-replicating mycobacteria, suggesting that accumulation of glucose-derived toxic metabolites does occur in the absence of sustained aerobic respiration. The culture medium traditionally used to study the physiology of hypoxic mycobacteria is supplemented with glucose. In this medium, M. tuberculosis can survive for only 7-10 days in a true non-replicating state before death is observed. By omitting glucose in the medium this period could be extended for up to at least 40 days without significant viability loss. Therefore, our study suggests that glycolysis leads to accumulation of glucose-derived toxic metabolites that limits long-term survival of hypoxic mycobacteria. Such toxic effect is exacerbated when the glycolytic pathway is disrupted at the PKF step.
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Affiliation(s)
- Wai Yee Phong
- Novartis Institute for Tropical Diseases, Singapore, Singapore
- Department of Microbiology, Immunology Programme, Yong Loo Lin School of Medicine, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Wenwei Lin
- Department of Microbiology, Immunology Programme, Yong Loo Lin School of Medicine, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Singapore-Massachusetts Institute of Technology Alliance for Research and Technology (SMART), CREATE NUS Campus, Singapore, Singapore
| | | | - Thomas Dick
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | - Sylvie Alonso
- Department of Microbiology, Immunology Programme, Yong Loo Lin School of Medicine, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Singapore-Massachusetts Institute of Technology Alliance for Research and Technology (SMART), CREATE NUS Campus, Singapore, Singapore
| | - Kevin Pethe
- Novartis Institute for Tropical Diseases, Singapore, Singapore
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168
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Weiner J, Maertzdorf J, Kaufmann SHE. The dual role of biomarkers for understanding basic principles and devising novel intervention strategies in tuberculosis. Ann N Y Acad Sci 2012. [PMID: 23181737 DOI: 10.1111/j.1749-6632.2012.06802.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
There is great need for better control measures for tuberculosis (TB). High-throughput analyses, such as transcriptomic and metabolic profiling, offer a promising path toward clinically useful biosignatures. With the help of biomarkers, it will be possible not only to reliably perform diagnosis but also to gain a better understanding of the disease process and, in the future, even predict the onset of disease in infected individuals. Biomarkers based on transcriptomic and metabolic profiles as well as on cytokine composition provide important insights into the basic biological principles of TB and give an opportunity to reliably distinguish TB patients from healthy individuals. Use of biomarkers for point-of-care diagnosis, however, is still a distant goal, which to achieve will require extensive analysis of TB biosignatures across different cohorts and a combination of different platforms.
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Affiliation(s)
- January Weiner
- Max Planck Institute for Infection Biology, Department of Immunology, Berlin, Germany
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169
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Abstract
Metabolomics has a special place among other 'omics' disciplines (genomics, transcriptomics and proteomics) as it describes the most dynamic level of biological regulation and, as such, provides the most direct reflection of the physiological status of an organism. Quick development of the analytical technologies in the first place - MS and NMR - has enabled the metabolomics analysis of such complex biological phenomena as host-pathogen interactions in the development of infection. In this review, an overview of the metabolomics studies of infectious diseases carried out on human material is provided. The relevant papers on the metabolomics of human infectious diseases are comprehensively summarized in a table, including, for example, information on the study design, number of subjects, employed technology and metabolic discriminator. Future considerations, such as importance of the time-resolved study designs and the embedment of metabolomics in large-scale epidemiological studies are discussed.
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170
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Wu B, Liu S, Guo X, Zhang Y, Zhang X, Li M, Cheng S. Responses of mouse liver to dechlorane plus exposure by integrative transcriptomic and metabonomic studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:10758-10764. [PMID: 22913625 DOI: 10.1021/es301804t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dechlorane plus (DP), a chlorinated flame retardant, has been widely detected in different environmental matrices and biota. However, toxicity data for DP have seldom been reported. In the present study, we investigated hepatic oxidative stress, DNA damage, and transcriptomic and metabonomic responses of male mice administered 500 mg/kg, 2000 mg/kg, and 5000 mg/kg of DP by gavage for 10 days. The results showed that DP exposure increased the level of superoxide dismutase (SOD) and 8-hydroxy-2-deoxyguanosine (8-OHdG). The microarray-based transcriptomic results demonstrated that DP exposure led to significant alteration of gene expression involved in carbohydrate, lipid, nucleotide, and energy metabolism, as well as signal transduction processes. The NMR-based metabonomic analyses corroborated these results showing changes of metabolites associated with the above altered mechanisms. Our results demonstrate that an oral exposure to DP can induce hepatic oxidative damage and perturbations of metabolism and signal transduction. These observations provide novel insight into toxicological effects and mechanisms of action of DP at the transcriptomic and metabonomic levels.
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Affiliation(s)
- Bing Wu
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, P.R. China.
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171
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Zinniel DK, Fenton RJ, Halouska S, Powers R, Barletta RG. Sample preparation of Mycobacterium tuberculosis extracts for nuclear magnetic resonance metabolomic studies. J Vis Exp 2012:e3673. [PMID: 22971839 DOI: 10.3791/3673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Mycobacterium tuberculosis is a major cause of mortality in human beings on a global scale. The emergence of both multi- (MDR) and extensively-(XDR) drug-resistant strains threatens to derail current disease control efforts. Thus, there is an urgent need to develop drugs and vaccines that are more effective than those currently available. The genome of M. tuberculosis has been known for more than 10 years, yet there are important gaps in our knowledge of gene function and essentiality. Many studies have since used gene expression analysis at both the transcriptomic and proteomic levels to determine the effects of drugs, oxidants, and growth conditions on the global patterns of gene expression. Ultimately, the final response of these changes is reflected in the metabolic composition of the bacterium including a few thousand small molecular weight chemicals. Comparing the metabolic profiles of wild type and mutant strains, either untreated or treated with a particular drug, can effectively allow target identification and may lead to the development of novel inhibitors with anti-tubercular activity. Likewise, the effects of two or more conditions on the metabolome can also be assessed. Nuclear magnetic resonance (NMR) is a powerful technology that is used to identify and quantify metabolic intermediates. In this protocol, procedures for the preparation of M. tuberculosis cell extracts for NMR metabolomic analysis are described. Cell cultures are grown under appropriate conditions and required Biosafety Level 3 containment, harvested, and subjected to mechanical lysis while maintaining cold temperatures to maximize preservation of metabolites. Cell lysates are recovered, filtered sterilized, and stored at ultra-low temperatures. Aliquots from these cell extracts are plated on Middlebrook 7H9 agar for colony-forming units to verify absence of viable cells. Upon two months of incubation at 37 °C, if no viable colonies are observed, samples are removed from the containment facility for downstream processing. Extracts are lyophilized, resuspended in deuterated buffer and injected in the NMR instrument, capturing spectroscopic data that is then subjected to statistical analysis. The procedures described can be applied for both one-dimensional (1D) H NMR and two-dimensional (2D) H-(13)C NMR analyses. This methodology provides more reliable small molecular weight metabolite identification and more reliable and sensitive quantitative analyses of cell extract metabolic compositions than chromatographic methods. Variations of the procedure described following the cell lysis step can also be adapted for parallel proteomic analysis.
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Affiliation(s)
- Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, USA
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172
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Weiner J, Parida SK, Maertzdorf J, Black GF, Repsilber D, Telaar A, Mohney RP, Arndt-Sullivan C, Ganoza CA, Faé KC, Walzl G, Kaufmann SHE. Biomarkers of inflammation, immunosuppression and stress with active disease are revealed by metabolomic profiling of tuberculosis patients. PLoS One 2012; 7:e40221. [PMID: 22844400 PMCID: PMC3402490 DOI: 10.1371/journal.pone.0040221] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/02/2012] [Indexed: 02/07/2023] Open
Abstract
Although tuberculosis (TB) causes more deaths than any other pathogen, most infected individuals harbor the pathogen without signs of disease. We explored the metabolome of >400 small molecules in serum of uninfected individuals, latently infected healthy individuals and patients with active TB. We identified changes in amino acid, lipid and nucleotide metabolism pathways, providing evidence for anti-inflammatory metabolomic changes in TB. Metabolic profiles indicate increased activity of indoleamine 2,3 dioxygenase 1 (IDO1), decreased phospholipase activity, increased abundance of adenosine metabolism products, as well as indicators of fibrotic lesions in active disease as compared to latent infection. Consistent with our predictions, we experimentally demonstrate TB-induced IDO1 activity. Furthermore, we demonstrate a link between metabolic profiles and cytokine signaling. Finally, we show that 20 metabolites are sufficient for robust discrimination of TB patients from healthy individuals. Our results provide specific insights into the biology of TB and pave the way for the rational development of metabolic biomarkers for TB.
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Affiliation(s)
- January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail: (SHEK); (JW)
| | - Shreemanta K. Parida
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jeroen Maertzdorf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Gillian F. Black
- Department of Biomedical Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Dirk Repsilber
- Biomathematics/Bioinformatics Group, Genetics and Biometry, Leibniz Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - Anna Telaar
- Biomathematics/Bioinformatics Group, Genetics and Biometry, Leibniz Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - Robert P. Mohney
- Metabolon, Inc., Durham, North Carolina, United States of America
| | | | - Christian A. Ganoza
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Kellen C. Faé
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Gerhard Walzl
- Department of Biomedical Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Stefan H. E. Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail: (SHEK); (JW)
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173
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Abstract
Microorganisms depend on their ability to modulate their metabolic composition according to specific circumstances, such as different phases of the growth cycle and circadian rhythms, fluctuations in environmental conditions, as well as experimental perturbations. A thorough understanding of these metabolic adaptations requires the ability to comprehensively identify and quantify the metabolome of bacterial cells in different states. In this review, we present an overview of the diverse metabolomics approaches recently adopted to explore the metabolism of a wide variety of microorganisms. Focusing on a selection of illustrative case studies, we assess the different experimental designs used and explore the major achievements and remaining challenges in the field. We conclude by discussing the important complementary information provided by computational methods such as genome-scale metabolic modeling, which enable an integrated analysis of metabolic state changes in the context of overall cellular physiology.
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174
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Wang X, Yang B, Zhang A, Sun H, Yan G. Potential drug targets on insomnia and intervention effects of Jujuboside A through metabolic pathway analysis as revealed by UPLC/ESI-SYNAPT-HDMS coupled with pattern recognition approach. J Proteomics 2011; 75:1411-27. [PMID: 22134358 DOI: 10.1016/j.jprot.2011.11.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/06/2011] [Accepted: 11/13/2011] [Indexed: 12/13/2022]
Abstract
Potential metabolites from the metabolic pathways could be therapeutic targets and useful for the discovery of broad spectrum drugs. UPLC/ESI-SYNAPT-HDMS coupled with pattern recognition methods including PCA, PLS-DA, OPLS-DA and Heatmap were integrated to examine the global metabolic signature of insomnia and intervention effects of Jujuboside A (JuA). Six unique pathways of the insomnia were identified using Ingenuity Pathway Analysis (IPA) software. The VIP-value threshold cutoff of the metabolites was set to 10, above this threshold, were filtered out as potential target biomarkers. Sixteen distinct metabolites were identified from these pathways, and 6 of them can be considered for rational drug design. It was further experimental validation that the changes in metabolic profiling were restored to their baseline values after JuA treatment according to the multivariate data analysis. Potential metabolite network of the insomnia was preliminarily predicted JuA-target interaction networks, and could be further explored for in silico docking studies with suitable drugs. Thus, our method is an efficient procedure for drug target identification through metabolic analysis. It can guide testable predictions, provide insights into drug action mechanisms and enable us to increase research productivity toward metabolomic drug discovery.
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Affiliation(s)
- Xijun Wang
- National TCM Key Lab of Serum Pharmacochemistry, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China.
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175
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Strelko CL, Lu W, Dufort FJ, Seyfried TN, Chiles TC, Rabinowitz JD, Roberts MF. Itaconic acid is a mammalian metabolite induced during macrophage activation. J Am Chem Soc 2011; 133:16386-9. [PMID: 21919507 DOI: 10.1021/ja2070889] [Citation(s) in RCA: 252] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Itaconic acid (ITA), or methylenesuccinic acid, is not generally classified as a mammalian metabolite. Using NMR-based metabolomics and (13)C-labeling, we have detected ITA in both macrophage-like VM-M3 and RAW 264.7 tumor cell lines as well as stimulated and unstimulated primary murine macrophages. Macrophage activation by addition of lipopolysaccharide and IFN-γ markedly increased ITA production and secretion. Crude cell extracts synthesize ITA via decarboxylation of cis-aconitate, indicative of a novel mammalian cis-aconitic decarboxylase activity. Our results highlight a previously unidentified biosynthetic pathway related to TCA cycle metabolism in mammalian cells and a novel metabolite that likely plays a role in macrophage-based immune response.
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Affiliation(s)
- Cheryl L Strelko
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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176
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Somashekar BS, Amin AG, Rithner CD, Troudt J, Basaraba R, Izzo A, Crick DC, Chatterjee D. Metabolic Profiling of Lung Granuloma in Mycobacterium tuberculosis Infected Guinea Pigs: Ex vivo 1H Magic Angle Spinning NMR Studies. J Proteome Res 2011; 10:4186-95. [DOI: 10.1021/pr2003352] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- B. S. Somashekar
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
| | - Anita G. Amin
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
| | - Christopher D. Rithner
- Central Instrument Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - JoLynn Troudt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
| | - Randall Basaraba
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
| | - Angelo Izzo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
| | - Dean C. Crick
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
| | - Delphi Chatterjee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1682, Fort Collins, Colorado 80523-1682, United States
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