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Multi Platforms Strategies and Metabolomics Approaches for the Investigation of Comprehensive Metabolite Profile in Dogs with Babesia canis Infection. Int J Mol Sci 2022; 23:ijms23031575. [PMID: 35163517 PMCID: PMC8835742 DOI: 10.3390/ijms23031575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
Canine babesiosis is an important tick-borne disease worldwide, caused by parasites of the Babesia genus. Although the disease process primarily affects erythrocytes, it may also have multisystemic consequences. The goal of this study was to explore and characterize the serum metabolome, by identifying potential metabolites and metabolic pathways in dogs naturally infected with Babesia canis using liquid and gas chromatography coupled to mass spectrometry. The study included 12 dogs naturally infected with B. canis and 12 healthy dogs. By combining three different analytical platforms using untargeted and targeted approaches, 295 metabolites were detected. The untargeted ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) metabolomics approach identified 64 metabolites, the targeted UHPLC-MS/MS metabolomics approach identified 205 metabolites, and the GC-MS metabolomics approach identified 26 metabolites. Biological functions of differentially abundant metabolites indicate the involvement of various pathways in canine babesiosis including the following: glutathione metabolism; alanine, aspartate, and glutamate metabolism; glyoxylate and dicarboxylate metabolism; cysteine and methionine metabolism; and phenylalanine, tyrosine, and tryptophan biosynthesis. This study confirmed that host–pathogen interactions could be studied by metabolomics to assess chemical changes in the host, such that the differences in serum metabolome between dogs with B. canis infection and healthy dogs can be detected with liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) methods. Our study provides novel insight into pathophysiological mechanisms of B. canis infection.
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Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations. PLoS Comput Biol 2021; 17:e1009234. [PMID: 34297714 PMCID: PMC8336858 DOI: 10.1371/journal.pcbi.1009234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/04/2021] [Accepted: 07/01/2021] [Indexed: 12/02/2022] Open
Abstract
Metabolic adaptations to complex perturbations, like the response to pharmacological treatments in multifactorial diseases such as cancer, can be described through measurements of part of the fluxes and concentrations at the systemic level and individual transporter and enzyme activities at the molecular level. In the framework of Metabolic Control Analysis (MCA), ensembles of linear constraints can be built integrating these measurements at both systemic and molecular levels, which are expressed as relative differences or changes produced in the metabolic adaptation. Here, combining MCA with Linear Programming, an efficient computational strategy is developed to infer additional non-measured changes at the molecular level that are required to satisfy these constraints. An application of this strategy is illustrated by using a set of fluxes, concentrations, and differentially expressed genes that characterize the response to cyclin-dependent kinases 4 and 6 inhibition in colon cancer cells. Decreases and increases in transporter and enzyme individual activities required to reprogram the measured changes in fluxes and concentrations are compared with down-regulated and up-regulated metabolic genes to unveil those that are key molecular drivers of the metabolic response. Deciphering the essential events in the reprogramming of metabolic networks subjected to complex perturbations, including the response to pharmacological treatments in multifactorial diseases like cancer, is crucial for the design of efficient therapies. Yet, tools to infer the molecular drivers sustaining such metabolic responses remain elusive for large metabolic networks. Here we develop an efficient computational strategy that integrates measured changes at systemic and molecular levels and combines metabolic control analysis with linear programming tools to infer key molecular drivers sustaining the metabolic adaptations to complex perturbations, such as an antitumoral drug therapy. The collective behavior is approximated using linear expressions where the adaptation of systemic concentrations and fluxes to a perturbation is described as a function of the molecular reprogramming of transport and enzyme activities. Starting from measured changes in fluxes and concentrations, we identify changes in the reprogramming of transporter and enzyme activities that are required to orchestrate the metabolic adaptation of colon cancer cells to a cell cycle inhibitor.
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Systems Biology and Biomarkers in Necrotizing Soft Tissue Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1294:167-186. [PMID: 33079369 DOI: 10.1007/978-3-030-57616-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
In necrotizing soft tissue infection (NSTI) there is a need to identify biomarker sets that can be used for diagnosis and disease management. The INFECT study was designed to obtain such insights through the integration of patient data and results from different clinically relevant experimental models by use of systems biology approaches. This chapter describes the current state of biomarkers in NSTI and how biomarkers are categorized. We introduce the fundamentals of top-down systems biology approaches including analysis tools and we review the use of current methods and systems biology approaches to biomarker discover. Further, we discuss how different "omics" signatures (gene expression, protein, and metabolites) from NSTI patient samples can be used to identify key host and pathogen factors involved in the onset and development of infection, as well as exploring associations to disease outcomes.
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Uppal K. Models of Metabolomic Networks. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11615-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Baer AG, Bourdon AK, Price JM, Campagna SR, Jacobson DA, Baghdoyan HA, Lydic R. Isoflurane anesthesia disrupts the cortical metabolome. J Neurophysiol 2020; 124:2012-2021. [PMID: 33112692 PMCID: PMC7814899 DOI: 10.1152/jn.00375.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Identifying similarities and differences in the brain metabolome during different states of consciousness has broad relevance for neuroscience and state-dependent autonomic function. This study focused on the prefrontal cortex (PFC) as a brain region known to modulate states of consciousness. Anesthesia was used as a tool to eliminate wakefulness. Untargeted metabolomic analyses were performed on microdialysis samples obtained from mouse PFC during wakefulness and during isoflurane anesthesia. Analyses detected 2,153 molecules, 91 of which could be identified. Analytes were grouped as detected during both wakefulness and anesthesia (n = 61) and as unique to wakefulness (n = 23) or anesthesia (n = 7). Data were analyzed using univariate and multivariate approaches. Relative to wakefulness, during anesthesia there was a significant (q < 0.0001) fourfold change in 21 metabolites. During anesthesia 11 of these 21 molecules decreased and 10 increased. The Kyoto Encyclopedia of Genes and Genomes database was used to relate behavioral state-specific changes in the metabolome to metabolic pathways. Relative to wakefulness, most of the amino acids and analogs measured were significantly decreased during isoflurane anesthesia. Nucleosides and analogs were significantly increased during anesthesia. Molecules associated with carbohydrate metabolism, maintenance of lipid membranes, and normal cell functions were significantly decreased during anesthesia. Significant state-specific changes were also discovered among molecules comprising lipids and fatty acids, monosaccharides, and organic acids. Considered together, these molecules regulate point-to-point transmission, volume conduction, and cellular metabolism. The results identify a novel ensemble of candidate molecules in PFC as putative modulators of wakefulness and the loss of wakefulness. NEW & NOTEWORTHY The loss of wakefulness caused by a single concentration of isoflurane significantly altered levels of interrelated metabolites in the prefrontal cortex. The results support the interpretation that states of consciousness reflect dynamic interactions among cortical neuronal networks involving a humbling number of molecules that comprise the brain metabolome.
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Affiliation(s)
- Aaron G Baer
- Department of Anesthesiology, University of Tennessee Medical Center, Knoxville, Tennessee
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Joshua M Price
- Office of Information Technology, University of Tennessee, Knoxville, Tennessee
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee.,Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, Tennessee
| | - Daniel A Jacobson
- Department of Psychology, University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Helen A Baghdoyan
- Department of Anesthesiology, University of Tennessee Medical Center, Knoxville, Tennessee.,Department of Psychology, University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Ralph Lydic
- Department of Anesthesiology, University of Tennessee Medical Center, Knoxville, Tennessee.,Department of Psychology, University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
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Carlsson H, Abujrais S, Herman S, Khoonsari PE, Åkerfeldt T, Svenningsson A, Burman J, Kultima K. Targeted metabolomics of CSF in healthy individuals and patients with secondary progressive multiple sclerosis using high-resolution mass spectrometry. Metabolomics 2020; 16:26. [PMID: 32052189 PMCID: PMC7015966 DOI: 10.1007/s11306-020-1648-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/01/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Standardized commercial kits enable targeted metabolomics analysis and may thus provide an attractive complement to the more explorative approaches. The kits are typically developed for triple quadrupole mass spectrometers using serum and plasma. OBJECTIVES Here we measure the concentrations of preselected metabolites in cerebrospinal fluid (CSF) using a kit developed for high-resolution mass spectrometry (HRMS). Secondarily, the study aimed to investigate metabolite alterations in patients with secondary progressive multiple sclerosis (SPMS) compared to controls. METHODS We performed targeted metabolomics in human CSF on twelve SPMS patients and twelve age and sex-matched healthy controls using the Absolute IDQ-p400 kit (Biocrates Life Sciences AG) developed for HRMS. The extracts were analysed using two methods; liquid chromatography-mass spectrometry (LC-HRMS) and flow injection analysis-MS (FIA-HRMS). RESULTS Out of 408 targeted metabolites, 196 (48%) were detected above limit of detection and 35 were absolutely quantified. Metabolites analyzed using LC-HRMS had a median coefficient of variation (CV) of 3% and 2.5% between reinjections the same day and after prolonged storage, respectively. The corresponding results for the FIA-HRMS were a median CV of 27% and 21%, respectively. We found significantly (p < 0.05) elevated levels of glycine, asymmetric dimethylarginine (ADMA), glycerophospholipid PC-O (34:0) and sum of hexoses in SPMS patients compared to controls. CONCLUSION The Absolute IDQ-p400 kit could successfully be used for quantifying targeted metabolites in the CSF. Metabolites quantified using LC-HRMS showed superior reproducibility compared to FIA-HRMS.
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Affiliation(s)
- Henrik Carlsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala University Hospital, Entrance 61, 3rd Floor, Dag Hammarskjölds Väg 18, 751 85, Uppsala, Sweden
| | - Sandy Abujrais
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala University Hospital, Entrance 61, 3rd Floor, Dag Hammarskjölds Väg 18, 751 85, Uppsala, Sweden
| | - Stephanie Herman
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala University Hospital, Entrance 61, 3rd Floor, Dag Hammarskjölds Väg 18, 751 85, Uppsala, Sweden
| | - Payam Emami Khoonsari
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala University Hospital, Entrance 61, 3rd Floor, Dag Hammarskjölds Väg 18, 751 85, Uppsala, Sweden
| | - Torbjörn Åkerfeldt
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala University Hospital, Entrance 61, 3rd Floor, Dag Hammarskjölds Väg 18, 751 85, Uppsala, Sweden
| | - Anders Svenningsson
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Burman
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala University Hospital, Entrance 61, 3rd Floor, Dag Hammarskjölds Väg 18, 751 85, Uppsala, Sweden.
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Wang X, Rezeng C, Wang Y, Li J, Zhang L, Chen J, Li Z. Toxicological Risks of Renqingchangjue in Rats Evaluated by 1H NMR-Based Serum and Urine Metabolomics Analysis. ACS OMEGA 2020; 5:2169-2179. [PMID: 32064377 PMCID: PMC7016918 DOI: 10.1021/acsomega.9b03084] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/17/2020] [Indexed: 05/09/2023]
Abstract
Renqingchangjue (RQCJ), a kind of Traditional Tibetan Medicine, has been widely utilized to treat various gastroenteritis diseases. However, the biosafety and toxicity of RQCJ was still indefinite because of toxic components in RQCJ, which included a variety of heavy metals. Thus, this study was aimed to evaluate the toxicity and expound the toxicological mechanism of RQCJ. In this study, rats were intragastrically administered with different doses of RQCJ for 15 days, and then, the restorative observation period lasted for 15 days. Liver and kidney tissues were collected for histopathological examination, and simultaneously serum and urine samples were collected for 1H nuclear magnetic resonance (1H NMR) spectroscopy analysis and biochemical analysis combined with inductively coupled plasma mass spectrometry (ICP-MS) measurement. The 1H NMR-based metabolomics analysis revealed that the administration of RQCJ significantly altered the concentrations of 14 serum metabolites and 14 urine metabolites, which implied disturbances in energy metabolism, amino acid metabolism, intestinal flora environment, and membrane damage. Besides, the biochemical analysis of serum samples was consistent with the histopathological results, which indicated slight hepatotoxicity and nephrotoxicity. The quantification of As and Hg in urine and serum samples by ICP-MS provided more evidence about the toxicity of RQCJ. This work provided an effective method to systematically and dynamically evaluate the toxicity of RQCJ and suggested that precautions should be taken in the clinic to monitor the potential toxicity of RQCJ.
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Affiliation(s)
- Xia Wang
- Department
of Chemistry, Capital Normal University, No. 105, Xisanhuanbeilu, Haidian District, Beijing 100048, PR China
| | - Caidan Rezeng
- College
of Pharmacy, Qinghai Nationalities University, No. 3 Bayizhong Road, Xining 810000, PR China
| | - Yingfeng Wang
- Department
of Chemistry, Capital Normal University, No. 105, Xisanhuanbeilu, Haidian District, Beijing 100048, PR China
| | - Jian Li
- Beijing
University of Chinese Medicine, No. 11 Beisanhuandonglu, Chaoyang District, Beijing 100029, PR China
| | - Lan Zhang
- Department
of Chemistry, Capital Normal University, No. 105, Xisanhuanbeilu, Haidian District, Beijing 100048, PR China
| | - Jianxin Chen
- Beijing
University of Chinese Medicine, No. 11 Beisanhuandonglu, Chaoyang District, Beijing 100029, PR China
| | - Zhongfeng Li
- Department
of Chemistry, Capital Normal University, No. 105, Xisanhuanbeilu, Haidian District, Beijing 100048, PR China
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Afzal M, Saccenti E, Madsen MB, Hansen MB, Hyldegaard O, Skrede S, Martins Dos Santos VAP, Norrby-Teglund A, Svensson M. Integrated Univariate, Multivariate, and Correlation-Based Network Analyses Reveal Metabolite-Specific Effects on Bacterial Growth and Biofilm Formation in Necrotizing Soft Tissue Infections. J Proteome Res 2020; 19:688-698. [PMID: 31833369 DOI: 10.1021/acs.jproteome.9b00565] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Necrotizing soft-tissue infections (NSTIs) have multiple causes, risk factors, anatomical locations, and pathogenic mechanisms. In patients with NSTI, circulating metabolites may serve as a substrate having impact on bacterial adaptation at the site of infection. Metabolic signatures associated with NSTI may reveal the potential to be useful as diagnostic and prognostic markers and novel targets for therapy. This study used untargeted metabolomics analyses of plasma from NSTI patients (n = 34) and healthy (noninfected) controls (n = 24) to identify the metabolic signatures and connectivity patterns among metabolites associated with NSTI. Metabolite-metabolite association networks were employed to compare the metabolic profiles of NSTI patients and noninfected surgical controls. Out of 97 metabolites detected, the abundance of 33 was significantly altered in NSTI patients. Analysis of metabolite-metabolite association networks showed a more densely connected network: specifically, 20 metabolites differentially connected between NSTI and controls. A selected set of significantly altered metabolites was tested in vitro to investigate potential influence on NSTI group A streptococcal strain growth and biofilm formation. Using chemically defined media supplemented with the selected metabolites, ornithine, ribose, urea, and glucuronic acid, revealed metabolite-specific effects on both bacterial growth and biofilm formation. This study identifies for the first time an NSTI-specific metabolic signature with implications for optimized diagnostics and therapies.
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Affiliation(s)
- Muhammad Afzal
- Center for Infectious Medicine, Department of Medicine, ANA Futura, Karolinska Institutet , Karolinska University Hospital , Alfred Nobels Allé 8 , 141 52 Huddinge , Sweden
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology , Wageningen University & Research , Stippeneng 4 , Wageningen 6708 WE , The Netherlands
| | - Martin Bruun Madsen
- Department of Intensive Care , Copenhagen University Hospital, Rigshospitalet , Copenhagen 2100 , Denmark
| | - Marco Bo Hansen
- Hyperbaric Unit, Department of Anesthesia, Center of Head and Orthopedics , Rigshospitalet, University of Copenhagen , Blegdamsvej 9 , Copenhagen DK-2100 , Denmark
| | - Ole Hyldegaard
- Department of Intensive Care , Copenhagen University Hospital, Rigshospitalet , Copenhagen 2100 , Denmark
| | - Steinar Skrede
- Department of Medicine , Haukeland University Hospital , Bergen N-5021 , Norway.,Department of Clinical Science , University of Bergen , Bergen N-5020 , Norway
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology , Wageningen University & Research , Stippeneng 4 , Wageningen 6708 WE , The Netherlands
| | - Anna Norrby-Teglund
- Center for Infectious Medicine, Department of Medicine, ANA Futura, Karolinska Institutet , Karolinska University Hospital , Alfred Nobels Allé 8 , 141 52 Huddinge , Sweden
| | - Mattias Svensson
- Center for Infectious Medicine, Department of Medicine, ANA Futura, Karolinska Institutet , Karolinska University Hospital , Alfred Nobels Allé 8 , 141 52 Huddinge , Sweden
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