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Kopriva I, Jerić I, Hadžija MP, Hadžija M, Lovrenčić MV. Non-negative Least Squares Approach to Quantification of 1H Nuclear Magnetic Resonance Spectra of Human Urine. Anal Chem 2021; 93:745-751. [PMID: 33284005 DOI: 10.1021/acs.analchem.0c02837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Because of its quantitative character and capability for high-throughput screening, 1H nuclear magnetic resonance (NMR) spectroscopy is used extensively in the profiling of biofluids such as urine and blood plasma. However, the narrow frequency bandwidth of 1H NMR spectroscopy leads to a severe overlap of the spectra of components present in the complex mixtures such as biofluids. Therefore, 1H NMR-based metabolomics analysis is focused on targeted studies related to concentrations of the small number of metabolites. Here, we propose a library-based approach to quantify proportions of overlapping metabolites from 1H NMR mixture spectra. The method boils down to the linear non-negative least squares (NNLS) problem, whereas proportions of the pure components contained in the library stand for the unknowns. The method is validated on an estimation of the proportions of (i) the 78 pure spectra, presumably related to type 2 diabetes mellitus (T2DM), from their synthetic linear mixture; (ii) metabolites present in 62 1H NMR spectra of urine of subjects with T2DM and 62 1H NMR spectra of urine of control subjects. In both cases, the in-house library of 210 pure component 1H NMR spectra represented the design matrix in the related NNLS problem. The proposed method pinpoints 63 metabolites that in a statistically significant way discriminate the T2DM group from the control group and 46 metabolites discriminating control from the T2DM group. For several T2DM-discriminative metabolites, we prove their presence by independent analytical determination or by pointing out the corresponding findings in the published literature.
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Affiliation(s)
- Ivica Kopriva
- Division of Electronics, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marijana Popović Hadžija
- Division of Molecular Medicine, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Mirko Hadžija
- Division of Molecular Medicine, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marijana Vučić Lovrenčić
- Department of Medical Biochemistry and Laboratory Medicine, University Hospital Merkur, Zajčeva 19, HR-10000 Zagreb, Croatia
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Holster S, Repsilber D, Geng D, Hyötyläinen T, Salonen A, Lindqvist CM, Rajan SK, de Vos WM, Brummer RJ, König J. Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. Benef Microbes 2020; 12:17-30. [PMID: 33350360 DOI: 10.3920/bm2020.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of a patient with the aim to restore a disturbed gut microbiota. In this study, it was investigated whether FMT has an effect on faecal microbial composition, its functional capacity, faecal metabolite profiles and their interactions in 16 irritable bowel syndrome (IBS) patients. Faecal samples from eight different time points before and until six months after allogenic FMT (faecal material from a healthy donor) as well as autologous FMT (own faecal material) were analysed by 16S RNA gene amplicon sequencing and gas chromatography coupled to mass spectrometry (GS-MS). The results showed that the allogenic FMT resulted in alterations in the microbial composition that were detectable up to six months, whereas after autologous FMT this was not the case. Similar results were found for the functional profiles, which were predicted from the phylogenetic sequencing data. While both allogenic FMT as well as autologous FMT did not have an effect on the faecal metabolites measured in this study, correlations between the microbial composition and the metabolites showed that the microbe-metabolite interactions seemed to be disrupted after allogenic FMT compared to autologous FMT. This shows that FMT can lead to altered interactions between the gut microbiota and its metabolites in IBS patients. Further research should investigate if and how this affects efficacy of FMT treatments.
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Affiliation(s)
- S Holster
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Repsilber
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Geng
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - T Hyötyläinen
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - A Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - C M Lindqvist
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - S K Rajan
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - W M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - R J Brummer
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J König
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
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53
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Ruszkiewicz DM, Sanders D, O'Brien R, Hempel F, Reed MJ, Riepe AC, Bailie K, Brodrick E, Darnley K, Ellerkmann R, Mueller O, Skarysz A, Truss M, Wortelmann T, Yordanov S, Thomas CLP, Schaaf B, Eddleston M. Diagnosis of COVID-19 by analysis of breath with gas chromatography-ion mobility spectrometry - a feasibility study. EClinicalMedicine 2020; 29:100609. [PMID: 33134902 PMCID: PMC7585499 DOI: 10.1016/j.eclinm.2020.100609] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is an urgent need to rapidly distinguish COVID-19 from other respiratory conditions, including influenza, at first-presentation. Point-of-care tests not requiring laboratory- support will speed diagnosis and protect health-care staff. We studied the feasibility of using breath-analysis to distinguish these conditions with near-patient gas chromatography-ion mobility spectrometry (GC-IMS). METHODS Independent observational prevalence studies at Edinburgh, UK, and Dortmund, Germany, recruited adult patients with possible COVID-19 at hospital presentation. Participants gave a single breath-sample for VOC analysis by GC-IMS. COVID-19 infection was identified by transcription polymerase chain reaction (RT- qPCR) of oral/nasal swabs together with clinical-review. Following correction for environmental contaminants, potential COVID-19 breath-biomarkers were identified by multi-variate analysis and comparison to GC-IMS databases. A COVID-19 breath-score based on the relative abundance of a panel of volatile organic compounds was proposed and tested against the cohort data. FINDINGS Ninety-eight patients were recruited, of whom 21/33 (63.6%) and 10/65 (15.4%) had COVID-19 in Edinburgh and Dortmund, respectively. Other diagnoses included asthma, COPD, bacterial pneumonia, and cardiac conditions. Multivariate analysis identified aldehydes (ethanal, octanal), ketones (acetone, butanone), and methanol that discriminated COVID-19 from other conditions. An unidentified-feature with significant predictive power for severity/death was isolated in Edinburgh, while heptanal was identified in Dortmund. Differentiation of patients with definite diagnosis (25 and 65) of COVID-19 from non-COVID-19 was possible with 80% and 81.5% accuracy in Edinburgh and Dortmund respectively (sensitivity/specificity 82.4%/75%; area-under-the-receiver- operator-characteristic [AUROC] 0.87 95% CI 0.67 to 1) and Dortmund (sensitivity / specificity 90%/80%; AUROC 0.91 95% CI 0.87 to 1). INTERPRETATION These two studies independently indicate that patients with COVID-19 can be rapidly distinguished from patients with other conditions at first healthcare contact. The identity of the marker compounds is consistent with COVID-19 derangement of breath-biochemistry by ketosis, gastrointestinal effects, and inflammatory processes. Development and validation of this approach may allow rapid diagnosis of COVID-19 in the coming endemic flu seasons. FUNDING MR was supported by an NHS Research Scotland Career Researcher Clinician award. DMR was supported by the University of Edinburgh ref COV_29.
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Affiliation(s)
- Dorota M Ruszkiewicz
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Daniel Sanders
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Rachel O'Brien
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Frederik Hempel
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Matthew J Reed
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
- Edinburgh Acute Care, Usher Institute of Population Health Sciences and Informatics, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ansgar C Riepe
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Kenneth Bailie
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Emma Brodrick
- IMSPEX Diagnostics Ltd, Ty Menter, Navigation Park, Abercynon, RCT CF45 4SN, United Kingdom
| | - Kareen Darnley
- Wellcome Clinical Research Facility, NHS Lothian, Edinburgh EH4 2XU, United Kingdom
| | | | - Oliver Mueller
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Angelika Skarysz
- Computer Science Department, School of Science, Loughborough University, United Kingdom
| | - Michael Truss
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Thomas Wortelmann
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Simeon Yordanov
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - C L Paul Thomas
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Bernhard Schaaf
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Michael Eddleston
- Pharmacology, Toxicology & Therapeutics, Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
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Ruszkiewicz DM, Sanders D, O'Brien R, Hempel F, Reed MJ, Riepe AC, Bailie K, Brodrick E, Darnley K, Ellerkmann R, Mueller O, Skarysz A, Truss M, Wortelmann T, Yordanov S, Thomas CLP, Schaaf B, Eddleston M. Diagnosis of COVID-19 by analysis of breath with gas chromatography-ion mobility spectrometry - a feasibility study. EClinicalMedicine 2020. [PMID: 33134902 DOI: 10.2139/ssrn.3675407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND There is an urgent need to rapidly distinguish COVID-19 from other respiratory conditions, including influenza, at first-presentation. Point-of-care tests not requiring laboratory- support will speed diagnosis and protect health-care staff. We studied the feasibility of using breath-analysis to distinguish these conditions with near-patient gas chromatography-ion mobility spectrometry (GC-IMS). METHODS Independent observational prevalence studies at Edinburgh, UK, and Dortmund, Germany, recruited adult patients with possible COVID-19 at hospital presentation. Participants gave a single breath-sample for VOC analysis by GC-IMS. COVID-19 infection was identified by transcription polymerase chain reaction (RT- qPCR) of oral/nasal swabs together with clinical-review. Following correction for environmental contaminants, potential COVID-19 breath-biomarkers were identified by multi-variate analysis and comparison to GC-IMS databases. A COVID-19 breath-score based on the relative abundance of a panel of volatile organic compounds was proposed and tested against the cohort data. FINDINGS Ninety-eight patients were recruited, of whom 21/33 (63.6%) and 10/65 (15.4%) had COVID-19 in Edinburgh and Dortmund, respectively. Other diagnoses included asthma, COPD, bacterial pneumonia, and cardiac conditions. Multivariate analysis identified aldehydes (ethanal, octanal), ketones (acetone, butanone), and methanol that discriminated COVID-19 from other conditions. An unidentified-feature with significant predictive power for severity/death was isolated in Edinburgh, while heptanal was identified in Dortmund. Differentiation of patients with definite diagnosis (25 and 65) of COVID-19 from non-COVID-19 was possible with 80% and 81.5% accuracy in Edinburgh and Dortmund respectively (sensitivity/specificity 82.4%/75%; area-under-the-receiver- operator-characteristic [AUROC] 0.87 95% CI 0.67 to 1) and Dortmund (sensitivity / specificity 90%/80%; AUROC 0.91 95% CI 0.87 to 1). INTERPRETATION These two studies independently indicate that patients with COVID-19 can be rapidly distinguished from patients with other conditions at first healthcare contact. The identity of the marker compounds is consistent with COVID-19 derangement of breath-biochemistry by ketosis, gastrointestinal effects, and inflammatory processes. Development and validation of this approach may allow rapid diagnosis of COVID-19 in the coming endemic flu seasons. FUNDING MR was supported by an NHS Research Scotland Career Researcher Clinician award. DMR was supported by the University of Edinburgh ref COV_29.
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Affiliation(s)
- Dorota M Ruszkiewicz
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Daniel Sanders
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Rachel O'Brien
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Frederik Hempel
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Matthew J Reed
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
- Edinburgh Acute Care, Usher Institute of Population Health Sciences and Informatics, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ansgar C Riepe
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Kenneth Bailie
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Emma Brodrick
- IMSPEX Diagnostics Ltd, Ty Menter, Navigation Park, Abercynon, RCT CF45 4SN, United Kingdom
| | - Kareen Darnley
- Wellcome Clinical Research Facility, NHS Lothian, Edinburgh EH4 2XU, United Kingdom
| | | | - Oliver Mueller
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Angelika Skarysz
- Computer Science Department, School of Science, Loughborough University, United Kingdom
| | - Michael Truss
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Thomas Wortelmann
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Simeon Yordanov
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - C L Paul Thomas
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Bernhard Schaaf
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Michael Eddleston
- Pharmacology, Toxicology & Therapeutics, Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
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Urinary 1H-NMR Metabolic Signature in Subjects Undergoing Colonoscopy for Colon Cancer Diagnosis. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10165401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolomics represents a promising non-invasive approach that can be applied to identify biochemical changes in colorectal cancer patients (CRC) and is potentially useful for diagnosis and follow-up. Despite the literature regarding metabolomics CRC-specific profiles, discrimination between metabolic changes specifically related to CRC and intra-individual variability is still a problem to be solved. This was a preliminary case-control study, in which 1H-NMR spectroscopy combined with multivariate statistical analysis was used to profile urine metabolites in subjects undergoing colonoscopy for colon cancer diagnosis. To reduce intra-individual variability, metabolic profiles were evaluated in participants’ urine samples, collected just before the colonoscopy and after a short-term dietary regimen required for the endoscopy procedure. Data obtained highlighted different urinary metabolic profiles between CRC and unaffected subjects (C). The metabolites altered in the CRC urine (acetoacetate, creatine, creatinine, histamine, phenylacetylglycine, and tryptophan) significantly correlated with colon cancer and discriminated with accuracy CRC patients from C patients (receiver operator characteristic (ROC) curve with an area under the curve (AUC) of 0.875; 95% CI: 0.667–1). These results confirm that urinary metabolomic analysis can be a valid tool to improve CRC diagnosis, prognosis, and response to therapy, representing a noninvasive approach that could precede more invasive tests.
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Ghaffari MH, Jahanbekam A, Post C, Sadri H, Schuh K, Koch C, Sauerwein H. Discovery of different metabotypes in overconditioned dairy cows by means of machine learning. J Dairy Sci 2020; 103:9604-9619. [PMID: 32747103 DOI: 10.3168/jds.2020-18661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/22/2020] [Indexed: 01/13/2023]
Abstract
Using data from targeted metabolomics in serum in combination with machine learning (ML) approaches, we aimed at (1) identifying divergent metabotypes in overconditioned cows and at (2) exploring how metabotypes are associated with lactation performance, blood metabolites, and hormones. In a previously established animal model, 38 pregnant multiparous Holstein cows were assigned to 2 groups that were fed differently to reach either high (HBCS) or normal (NBCS) body condition score (BCS) and backfat thickness (BFT) until dryoff at -49 d before calving [NBCS: BCS < 3.5 (3.02 ± 0.24) and BFT < 1.2 cm (0.92 ± 0.21), mean ± SD; HBCS: BCS > 3.75 (3.82 ± 0.33) and BFT > 1.4 cm (2.36 ± 0.35)]. Cows were then fed the same diets during the dry period and the subsequent lactation, and maintained the differences in BFT and BCS throughout the study. Blood samples were collected weekly from 7 wk antepartum (ap) to 12 wk postpartum (pp) to assess serum concentrations of metabolites (by targeted metabolomics and by classical analyses) and metabolic hormones. Metabolic clustering by applying 4 supervised ML-based classifiers [sequential minimal optimization (SMO), random forest (RF), alternating decision tree (ADTree), and naïve Bayes-updatable (NB)] on the changes (d 21 pp minus d 49 ap) in concentrations of 170 serum metabolites resulted in 4 distinct metabolic clusters: HBCS predicted HBCS (HBCS-PH, n = 13), HBCS predicted NBCS (HBCS-PN, n = 6), NBCS predicted NBCS (NBCS-PN, n = 15), and NBCS predicted HBCS (NBCS-PH, n = 4). The accuracies of SMO, RF, ADTree, and NB classifiers were >70%. Because the number of NBCS-PH cows was low, we did not consider this group for further comparisons. Dry matter intake (kg/d and percentage of body weight) and energy intake were greater in HBCS-PN than in HBCS-PH in early lactation, and HBCS-PN also reached a positive energy balance earlier than did HBCS-PH. Milk yield was not different between groups, but milk protein percentage was greater in HBCS-PN than in HBCS-PH cows. The circulating concentrations of fatty acids (FA) increased during early lactation in both groups, but HBCS-PN cows had lower concentrations of β-hydroxybutyrate, indicating lower ketogenesis compared with HBCS-PH cows. The concentrations of insulin, insulin-like growth factor 1, leptin, adiponectin, haptoglobin, glucose, and revised quantitative insulin sensitivity check index did not differ between the groups, whereas serum concentrations of glycerophospholipids were lower before calving in HBCS-PH than in HBCS-PN cows. Glycine was the only amino acid that had higher concentration after calving in HBCS-PH than in HBCS-PN cows. The circulating concentrations of some short- (C2, C3, and C4) and long-chain (C12, C16:0, C18:0, and C18:1) acylcarnitines on d 21 pp were greater in HBCS-PH than in HBCS-PN cows, indicating incomplete FA oxidation. In conclusion, the use of ML approaches involving data from targeted metabolomics in serum is a promising method for differentiating divergent metabotypes from apparently similar BCS phenotypes. Further investigations, using larger numbers of cows and farms, are warranted for confirmation of this finding.
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Affiliation(s)
- Morteza H Ghaffari
- Institute of Animal Science, Physiology Unit, University of Bonn, 53115 Bonn, Germany
| | | | - Christian Post
- Institute of Animal Science, Physiology Unit, University of Bonn, 53115 Bonn, Germany
| | - Hassan Sadri
- Department of Clinical Science, Faculty of Veterinary Medicine, University of Tabriz, 516616471 Tabriz, Iran
| | - Katharina Schuh
- Institute of Animal Science, Physiology Unit, University of Bonn, 53115 Bonn, Germany; Department of Life Sciences and Engineering, Animal Nutrition and Hygiene Unit, University of Applied Sciences Bingen, 55411 Bingen am Rhein, Germany
| | - Christian Koch
- Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, 67728 Münchweiler an der Alsenz, Germany
| | - Helga Sauerwein
- Institute of Animal Science, Physiology Unit, University of Bonn, 53115 Bonn, Germany.
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Abdallah HM, Ammar NM, Abdelhameed MF, Gendy AENGE, Ragab TIM, Abd-ElGawad AM, Farag MA, Alwahibi MS, Elshamy AI. Protective Mechanism of Acacia saligna Butanol Extract and Its Nano-Formulations against Ulcerative Colitis in Rats as Revealed via Biochemical and Metabolomic Assays. BIOLOGY 2020; 9:E195. [PMID: 32751448 PMCID: PMC7463518 DOI: 10.3390/biology9080195] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022]
Abstract
Ulcerative colitis (UC) is a relapsing inflammatory disease of unknown etiology. The increased risk of cancer in UC patients warrants for the development of novel drug treatments. Herein, this work concerns with the investigation of the protective effects of Acacia saligna butanol extract (ASBE) and its nanoformulations on UC in a rat model and its underlying mechanism. Colitis was induced by slow intrarectal infusion of 2 mL of 4% (v/v in 0.9% saline) acetic acid. Colon samples were evaluated macroscopically, microscopically, and assayed for pro-inflammatory cytokine levels. To monitor associated metabolic changes in acetic acid-induced UC model, serum samples were analyzed for primary metabolites using GC-MS followed by multivariate data analyses. Treatment with ASBE attenuated acetic acid-induced UC as revealed by reduction of colon weight, ulcer area, and ulcer index. ASBE treatment also reduced Cyclooxygenase-2 (COX-2), Prostaglandin E2 (PGE2) & Interleukin-1β (IL-1β) levels in the inflamed colon. The nano-formulation of ASBE showed better protection than the crude extract against ulcer indices, increased PGE2 production, and histopathological alterations such as intestinal mucosal lesions and inflammatory infiltration. Distinct metabolite changes were recorded in colitis rats including a decrease in oleamide and arachidonic acid along with increased levels of lactic acid, fructose, and pyroglutamic acid. Treatment with nano extract restored metabolite levels to normal and suggests that cytokine levels were regulated by nano extract in UC. Conclusion: ASBE nano extract mitigated against acetic acid-induced colitis in rats, and the underlying mechanism could be attributed to the modulatory effects of ASBE on the inflammatory cascades. The applicability of metabolomics developed in this rat model seems to be crucial for evaluating the anti-inflammatory mechanisms of new therapeutics for acute colitis.
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Affiliation(s)
- Heba M.I. Abdallah
- Pharmacology Department, Medical Research Division, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Naglaa M. Ammar
- Therapeutic Chemistry Department, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Mohamed F. Abdelhameed
- Pharmacology Department, Medical Research Division, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Abd El-Nasser G. El Gendy
- Medicinal and Aromatic Plants Research Department, National Research Center, Dokki, Giza 12622, Egypt;
| | - Tamer I. M. Ragab
- Chemistry of Natural and Microbial Products Department, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Ahmed M. Abd-ElGawad
- Plant Production Department, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Department of Botany, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini St., P.B., Cairo 11562, Egypt;
- Chemistry Department, School of Sciences & Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Mona S. Alwahibi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Abdelsamed I. Elshamy
- Department of Natural Compounds Chemistry, National Research Center, Dokki, Giza 12622, Egypt
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan
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Huang Z, Pan Z, Yang R, Bi Y, Xiong X. The canine gastrointestinal microbiota: early studies and research frontiers. Gut Microbes 2020; 11:635-654. [PMID: 31992112 PMCID: PMC7524387 DOI: 10.1080/19490976.2019.1704142] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The canine gut microbiota is a complex microbial population that is potentially related to metabolism, immunologic activity and gastrointestinal (GI) diseases. Early studies revealed that the canine gut microbiota was dynamic, and bacterial populations in the adjacent gut segments were similar, with anaerobes predominating. Metagenomics analysis revealed that nutrient contents in the diet modulated bacterial populations and metabolites in the canine gut. Further research revealed significant correlations between dietary factors and canine gut core microbiomes. Canine GI diseases are closely correlated with gut microbiota dysbiosis and metabolic disorders. Probiotic-related therapies can effectively treat canine GI diseases. Recent studies have revealed that the canine gut microbiota is similar to the human gut microbiota, and dietary factors affect both. Studying canine intestinal microorganisms enables clarifying changes in the canine intestinal bacteria under different conditions, simulating human diseases in dog models, and conducting in-depth studies of the interactions between intestinal bacteria and disease.
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Affiliation(s)
- Zongyu Huang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China,CONTACT Yujing Bi State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China,Xiaohui Xiong Nanjing Tech University, Nanjing, China
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Translational Potential of Metabolomics on Animal Models of Inflammatory Bowel Disease-A Systematic Critical Review. Int J Mol Sci 2020; 21:ijms21113856. [PMID: 32485793 PMCID: PMC7312423 DOI: 10.3390/ijms21113856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/16/2022] Open
Abstract
In the development of inflammatory bowel disease (IBD), the gut microbiota has been established as a key factor. Recently, metabolomics has become important for understanding the functional relevance of gut microbial changes in disease. Animal models for IBD enable the study of factors involved in disease development. However, results from animal studies may not represent the human situation. The aim of this study was to investigate whether results from metabolomics studies on animal models for IBD were similar to those from studies on IBD patients. Medline and Embase were searched for relevant studies up to May 2017. The Covidence systematic review software was used for study screening, and quality assessment was conducted for all included studies. Data showed a convergence of ~17% for metabolites differentiated between IBD and controls in human and animal studies with amino acids being the most differentiated metabolite subclass. The acute dextran sodium sulfate model appeared as a good model for analysis of systemic metabolites in IBD, but analytical platform, age, and biological sample type did not show clear correlations with any significant metabolites. In conclusion, this systematic review highlights the variation in metabolomics results, and emphasizes the importance of expanding the applied detection methods to ensure greater coverage and convergence between the various different patient phenotypes and animal models of inflammatory bowel disease.
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Benvenuti E, Pierini A, Gori E, Bartoli F, Erba P, Ruggiero P, Marchetti V. Serum amino acid profile in 51 dogs with immunosuppressant-responsive enteropathy (IRE): a pilot study on clinical aspects and outcomes. BMC Vet Res 2020; 16:117. [PMID: 32321505 PMCID: PMC7178940 DOI: 10.1186/s12917-020-02334-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/05/2020] [Indexed: 12/11/2022] Open
Abstract
Background Lower levels of tryptophan (TRP) have been identified in people with inflammatory bowel disease and in dogs with protein-losing enteropathy (PLE). No data on serum amino acids (AAs) but some on plasma in canine immunosuppressant-responsive enteropathy (IRE) are available. The aim of this study is to compare serum AAs between healthy and IRE dogs, considering clinicopathological variables and follow-up. Results Twenty-six healthy control dogs (CD) and 51 IRE dogs were included. IRE was diagnosed after the exclusion of extra-intestinal diseases and food and antibiotic responsive enteropathies. The canine chronic enteropathy clinical activity index (CCECAI) was assessed at presentation and during the clinical follow-up. In CD and IRE dogs, 19 different serum AAs were measured. IRE dogs were classified into responders, partial responders and non-responders, based on CCECAI after 1 month, and divided into PLE and non-PLE, based on albumin level. IRE dogs showed lower L-Tyrosine (TYR), L-Phenylalanine (PHE) and TRP (p < 0.001) and higher L-Serine (SER), L-Glutamic acid (GLU), L-Arginine (p < 0.001), L-Threonine (p = 0.013), Proline (p = 0.044), L-Cysteine (p = 0.003), L-Valine (p = 0.018), L-Lysine (p = 0.01) and L-Isoleucine (p = 0.005) than CDs. PLE dogs showed lower L-Histidine (HIS) (p = 0.008), PHE (p = 0.005) and TRP (p = 0.005) than non-PLE dogs. In IRE dogs, median GLU was significantly lower in dogs with BCS 3/9 than BCS 5/9 category (p = 0.036). Total protein was positively correlated with PHE and TRP (both p = 0.031, r = 0.30) and albumin was positively correlated with HIS (p = 0.025, r = 0.31), PHE and TRP (both p = 0.001, r = 0.46). HIS (p = 0.041), PHE (p = 0.047) and TRP (p = 0.044) concentrations were significantly lower in non-responders than in responders and partial responders. Conclusions This study may suggest further investigation on serum, HIS, PHE, TRP and TYR as markers of intestinal disease and proposed HIS, PHE and TRP as prognostic marker for response to therapy.
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Affiliation(s)
- Elena Benvenuti
- Department of Veterinary Science, University of Pisa, via Livornese, 56122 San Piero a Grado, Pisa, Italy
| | - Alessio Pierini
- Department of Veterinary Science, University of Pisa, via Livornese, 56122 San Piero a Grado, Pisa, Italy.
| | - Eleonora Gori
- Department of Veterinary Science, University of Pisa, via Livornese, 56122 San Piero a Grado, Pisa, Italy
| | - Francesco Bartoli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Savi, 10, Pisa, 56126, Italy
| | - Paola Erba
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Savi, 10, Pisa, 56126, Italy
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Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 2020; 17:223-237. [PMID: 32076145 DOI: 10.1038/s41575-019-0258-z] [Citation(s) in RCA: 911] [Impact Index Per Article: 227.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
A key role of the gut microbiota in the establishment and maintenance of health, as well as in the pathogenesis of disease, has been identified over the past two decades. One of the primary modes by which the gut microbiota interacts with the host is by means of metabolites, which are small molecules that are produced as intermediate or end products of microbial metabolism. These metabolites can derive from bacterial metabolism of dietary substrates, modification of host molecules, such as bile acids, or directly from bacteria. Signals from microbial metabolites influence immune maturation, immune homeostasis, host energy metabolism and maintenance of mucosal integrity. Alterations in the composition and function of the microbiota have been described in many studies on IBD. Alterations have also been described in the metabolite profiles of patients with IBD. Furthermore, specific classes of metabolites, notably bile acids, short-chain fatty acids and tryptophan metabolites, have been implicated in the pathogenesis of IBD. This Review aims to define the key classes of microbial-derived metabolites that are altered in IBD, describe the pathophysiological basis of these associations and identify future targets for precision therapeutic modulation.
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Preparation of Isotopically Labelled Standards of Creatinine Via H/D Exchange and Their Application in Quantitative Analysis by LC-MS. Molecules 2020; 25:molecules25071514. [PMID: 32225084 PMCID: PMC7180833 DOI: 10.3390/molecules25071514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 11/18/2022] Open
Abstract
Kidneys play a crucial role in maintaining metabolic homeostasis in a body. Serum creatinine concentration is a simple test used as an indicator of renal function. One of the known ways of quantifying creatinine concentration is the liquid chromatography-mass spectrometry (LC-MS) method, using an isotopically labeled analog of creatinine as an internal standard. Unfortunately, such isotope-labeled analogs are expensive and their synthesis is complex. Here we demonstrate a facile preparation of deuterated analogues of creatinine, via the H/D exchange of hydrogens located at the α-carbon (α-C) of the N-methylated amino acid part, under basic conditions. The stability of retrieved isotopologues was analyzed under both neutral or acidic conditions, and the results revealed that the introduced deuterons do not undergo back-exchange. In addition, the coelution of deuterated and non-deuterated forms under acidic and neutral conditions was observed. The prepared isotopologues were successfully applied in the quantitative LC-MS analysis of urine samples, and the results demonstrated that the presented strategy is novel and inexpensive, and that the quantification correlates with the commonly used Jaffe test method.
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Jeffery IB, Das A, O'Herlihy E, Coughlan S, Cisek K, Moore M, Bradley F, Carty T, Pradhan M, Dwibedi C, Shanahan F, O'Toole PW. Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption. Gastroenterology 2020; 158:1016-1028.e8. [PMID: 31843589 DOI: 10.1053/j.gastro.2019.11.301] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/16/2019] [Accepted: 11/01/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Irritable bowel syndrome (IBS) is a heterogeneous disorder, but diagnoses and determination of subtypes are made based on symptoms. We profiled the fecal microbiomes of patients with and without IBS to identify biomarkers of this disorder. METHODS We collected fecal and urine samples from 80 patients with IBS (Rome IV criteria; 16-70 years old) and 65 matched individuals without IBS (control individuals), along with anthropometric, medical, and dietary information. Shotgun and 16S ribosomal RNA amplicon sequencing were performed on feces, whereas urine and fecal metabolites were analyzed by gas chromatography and liquid chromatography-mass spectrometry. Co-occurrence networks were generated based on significant Spearman correlations between data. Bile acid malabsorption (BAM) was identified in patients with diarrhea by retention of radiolabeled selenium-75 homocholic acid taurine. RESULTS Patients with IBS had significant differences in network connections between diet and fecal microbiomes compared with control individuals; these were accompanied by differences in fecal metabolomes. We did not find significant differences in fecal microbiota composition among patients with different IBS symptom subtypes. Fecal metabolome profiles could discriminate patients with IBS from control individuals. Urine metabolomes also differed significantly between patients with IBS and control individuals, but most discriminatory metabolites were related to diet or medications. Fecal metabolomes, but not microbiomes, could distinguish patients with IBS with vs those without BAM. CONCLUSIONS Despite the heterogeneity of IBS, patients have significant differences in urine and fecal metabolomes and fecal microbiome vs control individuals, independent of symptom-based subtypes of IBS. Fecal metabolome analysis can be used to distinguish patients with IBS with vs those without BAM. These findings might be used for developing microbe-based treatments for these disorders.
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Affiliation(s)
- Ian B Jeffery
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Anubhav Das
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Eileen O'Herlihy
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Simone Coughlan
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Katryna Cisek
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Michael Moore
- Department of Radiology, Cork University Hospital, Cork, Ireland
| | - Fintan Bradley
- Medical Physics Department, Cork University Hospital, Cork, Ireland
| | - Tom Carty
- Medical Physics Department, Cork University Hospital, Cork, Ireland
| | - Meenakshi Pradhan
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Chinmay Dwibedi
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland
| | - Paul W O'Toole
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland; School of Microbiology, University College Cork, Ireland.
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Li X, Li M, Zheng R, Chen X, Xiang J, Wu FX, Wang J. Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification. Front Genet 2020; 10:1401. [PMID: 32117426 PMCID: PMC7013001 DOI: 10.3389/fgene.2019.01401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Since similar complex diseases are much alike in clinical symptoms, patients are easily misdiagnosed and mistreated. It is crucial to accurately predict the disease status and identify markers with high sensitivity and specificity for classifying similar complex diseases. Many approaches incorporating network information have been put forward to predict outcomes, but they are not robust because of their low reproducibility. Several pathway-based methods are robust and functionally interpretable. However, few methods characterize the disease-specific states of single samples from the perspective of pathways. In this study, we propose a novel framework, Pathway Activation for Single Sample (PASS), which utilizes the pathway information in a single sample way to better recognize the differences between two similar complex diseases. PASS can mainly be divided into two parts: for each pathway, the extent of perturbation of edges and the statistic difference of genes caused by a single disease sample are quantified; then, a novel method, named as an AUCpath, is applied to evaluate the pathway activation for single samples from the perspective of genes and their interactions. We have applied PASS to two main types of inflammatory bowel disease (IBD) and widely verified the characteristics of PASS. For a new patient, PASS features can be used as the indicators or potential pathway biomarkers to precisely diagnose complex diseases, discover significant features with interpretability and explore changes in the biological mechanisms of diseases.
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Affiliation(s)
- Xingyi Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Ruiqing Zheng
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Xiang Chen
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Ju Xiang
- School of Computer Science and Engineering, Central South University, Changsha, China.,Neuroscience Research Center & Department of Basic Medical Sciences, Changsha Medical University, Changsha, China
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, China
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Untargeted Serum Metabolic Profiling by Comprehensive Two-Dimensional Gas Chromatography–High-Resolution Time-of-Flight Mass Spectrometry. J Proteome Res 2019; 19:1013-1028. [DOI: 10.1021/acs.jproteome.9b00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Edouard Louis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
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Kopriva I, Jerić I, Hadžija MP, Hadžija M, Lovrenčić MV, Brkljačić L. Library-assisted nonlinear blind separation and annotation of pure components from a single 1H nuclear magnetic resonance mixture spectra. Anal Chim Acta 2019; 1080:55-65. [PMID: 31409475 DOI: 10.1016/j.aca.2019.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 01/07/2023]
Abstract
Due to its capability for high-throughput screening 1H nuclear magnetic resonance (NMR) spectroscopy is commonly used for metabolite research. The key problem in 1H NMR spectroscopy of multicomponent mixtures is overlapping of component signals and that is increasing with the number of components, their complexity and structural similarity. It makes metabolic profiling, that is carried out through matching acquired spectra with metabolites from the library, a hard problem. Here, we propose a method for nonlinear blind separation of highly correlated components spectra from a single 1H NMR mixture spectra. The method transforms a single nonlinear mixture into multiple high-dimensional reproducible kernel Hilbert Spaces (mRKHSs). Therein, highly correlated components are separated by sparseness constrained nonnegative matrix factorization in each induced RKHS. Afterwards, metabolites are identified through comparison of separated components with the library comprised of 160 pure components. Thereby, a significant number of them are expected to be related with diabetes type 2. Conceptually similar methodology for nonlinear blind separation of correlated components from two or more mixtures is presented in the Supplementary material. Single-mixture blind source separation is exemplified on: (i) annotation of five components spectra separated from one 1H NMR model mixture spectra; (ii) annotation of fifty five metabolites separated from one 1H NMR mixture spectra of urine of subjects with and without diabetes type 2. Arguably, it is for the first time a method for blind separation of a large number of components from a single nonlinear mixture has been proposed. Moreover, the proposed method pinpoints urinary creatine, glutamic acid and 5-hydroxyindoleacetic acid as the most prominent metabolites in samples from subjects with diabetes type 2, when compared to healthy controls.
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Affiliation(s)
- Ivica Kopriva
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Marijana Popović Hadžija
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Mirko Hadžija
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Marijana Vučić Lovrenčić
- Department of Medical Biochemistry and Laboratory Medicine, University Hospital Merkur, Zajčeva 19, HR-10000, Zagreb, Croatia
| | - Lidija Brkljačić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
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IRW and IQW Reduce Colitis-Associated Cancer Risk by Alleviating DSS-Induced Colonic Inflammation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6429845. [PMID: 31772935 PMCID: PMC6854911 DOI: 10.1155/2019/6429845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/21/2019] [Indexed: 12/26/2022]
Abstract
Background and Objective Bioactive peptides exert great influence in animals and human health by targeting gastrointestinal tracts. The colitis model of mice was induced by dextran sulfate sodium (DSS). Thirty-two 8-week-old mice weighing 23 g on average were randomly assigned to four groups of 8 each: mice fed basal diet (CON), mice fed basal diet with 5% DSS (DSS), mice fed 0.03% IRW with 5% DSS (IRW-DSS), and mice fed 0.03% IRW with 5% DSS (IQW-DSS). After an adaptation period of 3 days, on day 8, all mice were slaughtered. Serum samples were collected to determine the level of amino acids; colonic tissue was quick-frozen for the determination of gene expression. Methods The aim of this study was to assess the ability of two kinds of peptides (IRW and IQW) to repair intestinal inflammatory in the DSS-induced model in accordance with serum amino acids and intestinal inflammatory factors. Results The results demonstrated that the addition of IRW and IQW had a mitigating effect on DSS-induced intestinal inflammation. The level of Asp decreased in the serum of mice supplemented with IRW-DSS (P < 0.05), and IQW enhanced the level of Leu, but lowered the level of Ser (P < 0.05). IQW and IRW addition reduced the level of TNF-α and IL-17 (P < 0.05). No other significant effects were observed. Conclusions The present study demonstrated that intracolic administration of IRW and IQW might be a novel option for preventing inflammatory bowel disease via regulating the level of serum amino acid and enhancing the intestinal immune defense.
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Seo SH, Unno T, Park SE, Kim EJ, Lee YM, Na CS, Son HS. Korean Traditional Medicine ( Jakyakgamcho-tang) Ameliorates Colitis by Regulating Gut Microbiota. Metabolites 2019; 9:metabo9100226. [PMID: 31615012 PMCID: PMC6835967 DOI: 10.3390/metabo9100226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/10/2019] [Accepted: 10/12/2019] [Indexed: 02/07/2023] Open
Abstract
The objective of this study was to examine the anti-colitis activity of Jakyakgamcho-tang (JGT) in dextran sulfate sodium (DSS)-induced colitis and explore changes of the gut microbial community using 16S rRNA amplicon sequencing and metabolomics approaches. It was found that treatment with JGT or 5-aminosalicylic acid (5-ASA) alleviated the severity of colitis symptoms by suppressing inflammatory cytokine levels of IL-6, IL-12, and IFN-γ. The non-metric multidimensional scaling analysis of gut microbiome revealed that JGT groups were clearly separated from the DSS group, suggesting that JGT administration altered gut microbiota. The operational taxonomic units (OTUs) that were decreased by DSS but increased by JGT include Akkermansia and Allobaculum. On the other hand, OTUs that were increased by DSS but decreased by 5-ASA or JGT treatments include Bacteroidales S24-7, Ruminococcaceae, and Rikenellaceae, and the genera Bacteroides, Parabacteroides, Oscillospira, and Coprobacillus. After JGT administration, the metabolites, including most amino acids and lactic acid that were altered by colitis induction, became similar to those of the control group. This study demonstrates that JGT might have potential to effectively treat colitis by restoring dysbiosis of gut microbiota and host metabolites.
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Affiliation(s)
- Seung-Ho Seo
- School of Korean Medicine, Dongshin University, Naju 58245, Korea.
| | - Tatsuya Unno
- School of Life Sciences, Faculty of Biotechnology, SARI Jeju National University, Jeju 63243, Korea.
- Subtropical/tropical Organism Gene Bank Jeju National University, Jeju 63243, Korea.
| | - Seong-Eun Park
- School of Korean Medicine, Dongshin University, Naju 58245, Korea.
| | - Eun-Ju Kim
- School of Korean Medicine, Dongshin University, Naju 58245, Korea.
| | - Yu-Mi Lee
- School of Korean Medicine, Dongshin University, Naju 58245, Korea.
| | - Chang-Su Na
- School of Korean Medicine, Dongshin University, Naju 58245, Korea.
| | - Hong-Seok Son
- School of Korean Medicine, Dongshin University, Naju 58245, Korea.
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Profiling of Amino Acids in Urine Samples of Patients Suffering from Inflammatory Bowel Disease by Capillary Electrophoresis-Mass Spectrometry. Molecules 2019; 24:molecules24183345. [PMID: 31540027 PMCID: PMC6767150 DOI: 10.3390/molecules24183345] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Urine represents a convenient biofluid for metabolomic studies due to its noninvasive collection and richness in metabolites. Here, amino acids are valuable biomarkers for their ability to reflect imbalances of different biochemical pathways. An impact of amino acids on pathology, prognosis and therapy of various diseases, including inflammatory bowel disease (IBD), is therefore the subject of current clinical research. This work is aimed to develop a capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) method for the quantification of the 20 proteinogenic amino acids in human urine samples obtained from patients suffering from IBD and treated with thiopurines. The optimized CE-MS/MS method, with minimum sample preparation (just “dilute and shoot”), exhibited excellent linearity for all the analytes (coefficients of determination were higher than 0.99), with inter-day and intra-day precision yielding relative standard deviations in the range of 0.91–15.12% and with accuracy yielding relative errors in the range of 85.47–112.46%. Total analysis time, an important parameter for the sample throughput demanded in routine practice, was shorter in ca. 17% when compared to established CE-MS methods. Favorable performance of the proposed CE-MS/MS method was also confirmed by the comparison with corresponding ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) method. Consistent data for the investigated amino acid metabolome were obtained using both methods. For the first time, the amino acid profiling by CE-MS approach was applied on the clinical IBD samples. Here, significant differences observed in the concentration levels of some amino acids between IBD patients undergoing thiopurine treatment and healthy volunteers could result from the simultaneous action of the disease and the corresponding therapy. These findings indicate that amino acids analysis could be a valuable tool for the study of mechanism of the IBD treatment by thiopurines.
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Fatima T, Hashmi S, Iqbal A, Siddiqui AJ, Sami SA, Basir N, Bokhari SS, Sharif H, Musharraf SG. Untargeted metabolomic analysis of coronary artery disease patients with diastolic dysfunction show disturbed oxidative pathway. Metabolomics 2019; 15:98. [PMID: 31236740 DOI: 10.1007/s11306-019-1559-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/17/2019] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Left ventricular diastolic dysfunction (LVDD) is common in patients with coronary artery disease (CAD) with prevalence estimates of 34% and constitutes a predictor of all-cause mortality. Although diastolic dysfunction is induced by myocardial ischemia and has been shown to alter the clinical course, the role of coronary artery disease in the diastolic dysfunction and its progression into heart failure has not been completely elucidated. OBJECTIVE The present study was conducted to identify possible metabolites in coronary artery disease patients that are differentially regulated in patients with diastolic dysfunction. METHODS The serum of CAD (n = 75) patients and young healthy volunteers (n = 43) were analysed by using gas chromatography mass spectrometry (GC-MS) technique. Pre-processing of data results in 1547 features; among them 1064 features were annotated using NIST library. RESULTS AND CONCLUSION Fifteen metabolites were found to be statistically different between cases and control. Variation in metabolites were identified and correlated with several clinically important echocardiography parameters i.e. LVDD grades, ejection fraction (EF) and E/e' values. The results suggested that metabolic products of fatty acid oxidation and glucose oxidation pathways such as oleic acid, stearic acid, palmitic acid, linoleic acid, galactose, pyruvic and lactic acids are predominantly up regulated in patients with coronary artery disease and severity of diastolic dysfunction appears to be linked to increase in fatty acid oxidation and inflammation. The metabolic fingerprints of these patients give us an insight into the pathophysiological mechanism of diastolic dysfunction in coronary artery disease patients although it did not identify validated novel markers.
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Affiliation(s)
- Tamkeen Fatima
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Satwat Hashmi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Ayesha Iqbal
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Amna Jabbar Siddiqui
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Shahid A Sami
- Department of Surgery, Aga Khan University, Karachi, Pakistan
| | - Najeeb Basir
- Department of Medicine, Aga Khan University, Karachi, Pakistan
| | | | - Hasanat Sharif
- Department of Surgery, Aga Khan University, Karachi, Pakistan
| | - Syed Ghulam Musharraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Li X, Wang L, Ma H. Betaine alleviates high glucose‑induced mesangial cell proliferation by inhibiting cell proliferation and extracellular matrix deposition via the AKT/ERK1/2/p38 MAPK pathway. Mol Med Rep 2019; 20:1754-1760. [PMID: 31257485 PMCID: PMC6625408 DOI: 10.3892/mmr.2019.10391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/14/2019] [Indexed: 12/16/2022] Open
Abstract
Diabetic nephropathy (DN) is a major cause of chronic renal failure in diabetic patients worldwide. Betaine, a zwitterionic quaternary ammonium salt compound, is involved in numerous biological processes. The present study aimed to investigate the effects of betaine on mouse mesangial cells (MMCs) cultured under high glucose (HG) conditions and its underlying mechanisms. MMCs were treated with betaine under HG conditions. Cell proliferation and the cell cycle distribution were investigated with an MTT assay and flow cytometry, respectively. Western blotting and reverse transcription‑quantitative polymerase chain reaction analyses were applied to respectively determine protein and mRNA expression levels. The results suggested that betaine decreased cell proliferation in a dose‑dependent manner, while G1‑phase arrest was significantly induced in MMCs. Compared with the control group, the expression levels of p21 and p27 decreased under HG conditions, but were reversed by betaine. Furthermore, the expression levels of fibronectin and type IV collagen were significantly decreased in cells treated with betaine compared with the HG group. Additionally, betaine decreased the phosphorylation of Akt, extracellular‑signal‑regulated kinase (Erk)1/2 and p38 mitogen‑activated protein kinase (MAPK), but was enhanced under HG conditions. Overall, the results of the present study indicated that betaine serves a protective role in HG‑induced MMCs by inhibiting cell proliferation and extracellular matrix deposition via regulating regulation of the Akt/Erk1/2/p38 MAPK signaling pathway.
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Affiliation(s)
- Xianhui Li
- Department of Traditional Chinese Medicine, Tianjin Key Laboratory of Artificial Cell, Tianjin Institute of Hepatobiliary Disease, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Third Central Hospital of Tianjin, Tianjin 300170, P.R. China
| | - Li Wang
- Department of Basic Medicine, Tianjin Medical College, Tianjin 300222, P.R. China
| | - Huining Ma
- Department of Traditional Chinese Medicine, Tianjin 4th Centre Hospital, Tianjin 300140, P.R. China
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Iaccarino N, Amato J, Pagano B, Di Porzio A, Micucci M, Bolelli L, Aldini R, Novellino E, Budriesi R, Randazzo A. Impact of phytosterols on liver and distal colon metabolome in experimental murine colitis model: an explorative study. J Enzyme Inhib Med Chem 2019; 34:1041-1050. [PMID: 31074304 PMCID: PMC6522980 DOI: 10.1080/14756366.2019.1611802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Phytosterols are known to reduce plasma cholesterol levels and thereby reduce cardiovascular risk. Studies conducted on human and animal models have demonstrated that these compounds have also anti-inflammatory effects. Recently, an experimental colitis model (dextran sulphate sodium-induced) has shown that pre-treatment with phytosterols decreases infiltration of inflammatory cells and accelerates mucosal healing. This study aims to understand the mechanism underlying the colitis by analysing the end-products of the metabolism in distal colon and liver excised from the same mice used in the previous work. In particular, an unsupervised gas chromatography-mass spectrometry (GC-MS) and NMR based metabolomics approach was employed to identify the metabolic pathways perturbed by the dextran sodium sulphate (DSS) insult (i.e. Krebs cycle, carbohydrate, amino acids, and nucleotide metabolism). Interestingly, phytosterols were able to restore the homeostatic equilibrium of the hepatic and colonic metabolome.
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Affiliation(s)
- Nunzia Iaccarino
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Jussara Amato
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Bruno Pagano
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Anna Di Porzio
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Matteo Micucci
- b Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Luca Bolelli
- b Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Rita Aldini
- b Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Ettore Novellino
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Roberta Budriesi
- b Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Antonio Randazzo
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
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Ghosh N, Choudhury P, Subramani E, Saha D, Sengupta S, Joshi M, Banerjee R, Roychowdhury S, Bhattacharyya P, Chaudhury K. Metabolomic signatures of asthma-COPD overlap (ACO) are different from asthma and COPD. Metabolomics 2019; 15:87. [PMID: 31165288 DOI: 10.1007/s11306-019-1552-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Asthma-chronic obstructive pulmonary disease (COPD) overlap, termed as ACO, is a complex heterogeneous disease without any clear diagnostic or therapeutic guidelines. The pathophysiology of the disease, its characteristic features, and existence as a unique disease entity remains unclear. Individuals with ACO have a faster lung function decline, more frequent exacerbations, and worse quality of life than those with COPD or asthma alone. OBJECTIVES The present study aims to determine whether ACO has a distinct metabolic profile in comparison to asthma and COPD. METHODS Two different groups of patients were recruited as discovery (D) and validation (V) cohorts. Serum samples obtained from moderate and severe asthma patients diagnosed as per GINA guidelines [n = 34(D); n = 32(V)], moderate and severe COPD cases identified by GOLD guidelines [n = 30(D); 32(V)], ACO patients diagnosed by joint GOLD and GINA guidelines [n = 35(D); 40(V)] and healthy controls [n = 33(D)] were characterized using nuclear magnetic resonance (NMR) spectrometry. RESULTS Multivariate and univariate analysis indicated that 12 metabolites [lipid, isoleucine, N-acetylglycoproteins (NAG), valine, glutamate, citric acid, glucose, L-leucine, lysine, asparagine, phenylalanine and histidine] were dysregulated in ACO patients when compared with both asthma and COPD. These metabolites were further validated in a fresh cohort of patients, which again exhibited a similar expression pattern. CONCLUSIONS Our findings suggest that ACO has an enhanced energy and metabolic burden associated with it as compared to asthma and COPD. It is anticipated that our results will stimulate researchers to further explore ACO and unravel the pathophysiological complexities associated with the disease.
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Affiliation(s)
- Nilanjana Ghosh
- School of Medical Science and Technology (SMST), Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Priyanka Choudhury
- School of Medical Science and Technology (SMST), Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Elavarasan Subramani
- School of Medical Science and Technology (SMST), Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | | | | | - Mamata Joshi
- National Facility for High-field NMR, Tata Institute of Fundamental Research, Mumbai, India
| | - Rintu Banerjee
- Department of Agricultural & Food Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | | | - Koel Chaudhury
- School of Medical Science and Technology (SMST), Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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74
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Gardner A, Parkes HG, So PW, Carpenter GH. Determining bacterial and host contributions to the human salivary metabolome. J Oral Microbiol 2019; 11:1617014. [PMID: 34109015 PMCID: PMC7610937 DOI: 10.1080/20002297.2019.1617014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: Salivary metabolomics is rapidly advancing. Aim and methods: To determine the extent to which salivary metabolites reflects host or microbial metabolic activity whole-mouth saliva (WMS), parotid saliva (PS) and plasma collected contemporaneously from healthy volunteers were analysed by 1H-NMR spectroscopy. Spectra underwent principal component analysis and k-means cluster analysis and metabolite quantification. WMS samples were cultured on both sucrose and peptide-enriched media. Correlation between metabolite concentration and bacterial load was assessed. Results: WMS contained abundant short-chain fatty acids (SCFAs), which were minimal in PS and plasma. WMS spectral exhibited greater inter-individual variation than those of PS or plasma (6.7 and 3.6 fold, respectively), likely reflecting diversity of microbial metabolomes. WMS bacterial load correlated strongly with SCFA levels. Additional WMS metabolites including amines, amino acids and organic acids were positively correlated with bacterial load. Lactate, urea and citrate appeared to enter WMS via PS and the circulation. Urea correlated inversely with WMS bacterial load. Conclusions: Oral microbiota contribute significantly to the WMS metabolome. Several WMS metabolites (lactate, urea and citrate) are derived from the host circulation. WMS may be particularly useful to aid diagnosis of conditions reflective of dysbiosis. WMS could also complement other gastrointestinal fluids in future metabolomic studies.
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Affiliation(s)
- Alexander Gardner
- Department of Mucosal and Salivary Biology, Dental Institute, King's College London, London, UK
| | - Harold G Parkes
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - Po-Wah So
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Guy H Carpenter
- Department of Mucosal and Salivary Biology, Dental Institute, King's College London, London, UK
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Pontes TA, Barbosa AD, Silva RD, Melo-Junior MR, Silva RO. Osteopenia-osteoporosis discrimination in postmenopausal women by 1H NMR-based metabonomics. PLoS One 2019; 14:e0217348. [PMID: 31141566 PMCID: PMC6541380 DOI: 10.1371/journal.pone.0217348] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
This is a report on how 1H NMR-based metabonomics was employed to discriminate osteopenia from osteoporosis in postmenopausal women, identifying the main metabolites associated to the separation between the groups. The Assays were performed using seventy-eight samples, being twenty-eight healthy volunteers, twenty-six osteopenia patients and twenty-four osteoporosis patients. PCA, LDA, PLS-DA and OPLS-DA formalisms were used. PCA discriminated the samples from healthy volunteers from diseased patient samples. Osteopenia-osteoporosis discrimination was only obtained using Analysis Discriminants formalisms, as LDA, PLS-DA and OPLS-DA. The metabonomics model using LDA formalism presented 88.0% accuracy, 88.5% specificity and 88.0% sensitivity. Cross-Validation, however, presented some problems as the accuracy of modeling decreased. LOOCV resulted in 78.0% accuracy. The OPLS-DA based model was better: R2Y and Q2 values equal to 0.871 (p<0.001) and 0.415 (p<0.001). LDA and OPLS-DA indicated the important spectral regions for discrimination, making possible to assign the metabolites involved in the skeletal system homeostasis, as follows: VLDL, LDL, leucine, isoleucine, allantoin, taurine and unsaturated lipids. These results indicate that 1H NMR-based metabonomics can be used as a diagnosis tool to discriminate osteoporosis from osteopenia using a single serum sample.
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Affiliation(s)
- T. A. Pontes
- Biology Applied to Health Postgraduate Program. LIKA–Laboratory of Immunopatology Keizo Asami. Universidade Federal de Pernambuco, Av Prof Luis Freire, s/n. Cidade Universitaria, Recife-PE, Brazil
- * E-mail:
| | - A. D. Barbosa
- Biology Applied to Health Postgraduate Program. LIKA–Laboratory of Immunopatology Keizo Asami. Universidade Federal de Pernambuco, Av Prof Luis Freire, s/n. Cidade Universitaria, Recife-PE, Brazil
| | - R. D. Silva
- Fundamental Chemistry Department, CCEN. Chemistry Postgraduate Program. Universidade Federal de Pernambuco. Av. Jornalista Aníbal Fernandes, s/n. Cidade Universitária, Recife-PE, Brazil
| | - M. R. Melo-Junior
- Biology Applied to Health Postgraduate Program. LIKA–Laboratory of Immunopatology Keizo Asami. Universidade Federal de Pernambuco, Av Prof Luis Freire, s/n. Cidade Universitaria, Recife-PE, Brazil
| | - R. O. Silva
- Fundamental Chemistry Department, CCEN. Chemistry Postgraduate Program. Universidade Federal de Pernambuco. Av. Jornalista Aníbal Fernandes, s/n. Cidade Universitária, Recife-PE, Brazil
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76
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Abdul Ghani ZDF, Ab Rashid AH, Shaari K, Chik Z. Urine NMR Metabolomic Study on Biochemical Activities to Investigate the Effect of P. betle Extract on Obese Rats. Appl Biochem Biotechnol 2019; 189:690-708. [DOI: 10.1007/s12010-019-03042-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022]
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Pietzke M, Arroyo SF, Sumpton D, Mackay GM, Martin-Castillo B, Camps J, Joven J, Menendez JA, Vazquez A. Stratification of cancer and diabetes based on circulating levels of formate and glucose. Cancer Metab 2019; 7:3. [PMID: 31049200 PMCID: PMC6482583 DOI: 10.1186/s40170-019-0195-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Serum and urine metabolites have been investigated for their use as cancer biomarkers. The specificity of candidate metabolites can be limited by the impact of other disorders on metabolite levels. In particular, the increasing incidence of obesity could become a significant confounding factor. METHODS Here we developed a multinomial classifier for the stratification of cancer, obesity and healthy phenotypes based on circulating glucose and formate levels. We quantified the classifier performance from the retrospective analysis of samples from breast cancer, lung cancer, obese individuals and healthy controls. RESULTS We discovered that circulating formate levels are significantly lower in breast and lung cancer patients than in healthy controls. However, the performance of a cancer classifier based on formate levels alone is limited because obese patients also have low serum formate levels. By introducing a multinomial classifier based on circulating glucose and formate levels, we were able to improve the classifier performance, reaching a true positive rate of 79% with a false positive rate of 8%. CONCLUSIONS Circulating formate is reduced in HER2+ breast cancer, non-small cell lung cancer and highly obese patients relative to healthy controls. Further studies are required to determine the relevance of these observations in other cancer types and diseases.
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Affiliation(s)
- Matthias Pietzke
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow, G61 1BD UK
| | - Salvador Fernandez Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | - David Sumpton
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow, G61 1BD UK
| | - Gillian M. Mackay
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow, G61 1BD UK
| | | | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | - Javier A. Menendez
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, Girona, Catalonia Spain
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Alexei Vazquez
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow, G61 1BD UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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78
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Wesley UV, Bhute VJ, Hatcher JF, Palecek SP, Dempsey RJ. Local and systemic metabolic alterations in brain, plasma, and liver of rats in response to aging and ischemic stroke, as detected by nuclear magnetic resonance (NMR) spectroscopy. Neurochem Int 2019; 127:113-124. [PMID: 30707914 DOI: 10.1016/j.neuint.2019.01.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/29/2019] [Indexed: 12/12/2022]
Abstract
Metabolic dysfunction impacts stroke incidence and outcome. However, the intricate association between altered metabolic program due to aging, and focal ischemia in brain, circulation, and peripheral organs is not completely elucidated. Here we identified locally and systemically altered metabolites in brain, liver, and plasma as a result of normal aging, ischemic-stroke, and extended time of reperfusion injury. Comprehensive quantitative metabolic profiling was carried out using nuclear magnetic resonance spectroscopy. Aging, but healthy rats showed significant metabolic alterations in the brain, but only a few metabolic changes in the liver and plasma as compared to younger rats. But, ischemic stroke altered metabolites significantly in liver and plasma of older rats during early acute phase. Major metabolic changes were also seen in the brains of younger rats following ischemic stroke during early acute phase of injury. We further report that metabolic changes occur sequentially in a tissue specific manner during extended reperfusion time of late repair phase. First metabolic alterations occurred in brain due to local injury. Next, changes in circulating metabolites in plasma occurred during acute-repair phase transition time. Lastly, the delayed systemic effect was seen in the peripheral organ, liver that exhibited significant and persistent changes in selected metabolites during later reperfusion time. The metabolic pathways involved in energy/glucose, and amino acid metabolism, inflammation, and oxidative stress were mainly altered as a result of aging and ischemia/reperfusion. Biomarker analysis revealed citrate, lysine, and tyrosine as potential age-independent blood metabolic biomarkers of ischemia/reperfusion. Overall, our study elucidates the complex network of metabolic events as a function of normal aging and acute stroke. We further provide evidence for a clear transition from local to systemic metabolic dysfunction due to ischemic injury in a time dependent manner, which may altogether greatly impact the post-stroke outcome.
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Affiliation(s)
- Umadevi V Wesley
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA.
| | - Vijesh J Bhute
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, 53792, USA
| | - James F Hatcher
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, 53792, USA
| | - Robert J Dempsey
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA
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Segal JP, Mullish BH, Quraishi MN, Acharjee A, Williams HRT, Iqbal T, Hart AL, Marchesi JR. The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease. Therap Adv Gastroenterol 2019; 12:1756284818822250. [PMID: 30719076 PMCID: PMC6348496 DOI: 10.1177/1756284818822250] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/23/2018] [Indexed: 02/04/2023] Open
Abstract
The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD.
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Affiliation(s)
- Jonathan P. Segal
- Inflammatory Bowel Disease Department, St Mark’s Hospital, Harrow HA1 3UJ, UK
| | - Benjamin H. Mullish
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, UK
| | - Mohammed Nabil Quraishi
- Institute of Immunology and Immunotherapy, University of Birmingham, Department of Gastroenterology, University Hospital, Birmingham, UK
| | - Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
| | - Horace R. T. Williams
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, UK
| | - Tariq Iqbal
- Institute of Immunology and Immunotherapy, University of Birmingham, Department of Gastroenterology, University Hospital, Birmingham, UK
| | - Ailsa L. Hart
- Inflammatory Bowel Disease Department, St Mark’s Hospital, Harrow, UK
- Department of Surgery and Cancer, Division of Integrative Systems Medicine and Digestive Disease, Faculty of Medicine, Imperial College, London, UK
| | - Julian R. Marchesi
- Department of Surgery and Cancer, Division of Integrative Systems Medicine and Digestive Disease, Faculty of Medicine, Imperial College, London, UK
- School of Biosciences, Cardiff University, Cardiff, UK
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. High-Throughput Metabolomics by 1D NMR. Angew Chem Int Ed Engl 2019; 58:968-994. [PMID: 29999221 PMCID: PMC6391965 DOI: 10.1002/anie.201804736] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.
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Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P.Via Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Veronica Ghini
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Gaia Meoni
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Cristina Licari
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of FlorenceLargo Brambilla 3FlorenceItaly
| | - Paola Turano
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| | - Claudio Luchinat
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
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Sugihara K, Morhardt TL, Kamada N. The Role of Dietary Nutrients in Inflammatory Bowel Disease. Front Immunol 2019; 9:3183. [PMID: 30697218 PMCID: PMC6340967 DOI: 10.3389/fimmu.2018.03183] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/27/2018] [Indexed: 12/22/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and relapsing inflammatory disease of the gastrointestinal tract. Although the precise etiology of IBD remains incompletely understood, accumulating evidence suggests that various environmental factors, including dietary nutrients, contribute to its pathogenesis. Dietary nutrients are known to have an impact on host physiology and diseases. The interactions between dietary nutrients and intestinal immunity are complex. Dietary nutrients directly regulate the immuno-modulatory function of gut-resident immune cells. Likewise, dietary nutrients shape the composition of the gut microbiota. Therefore, a well-balanced diet is crucial for good health. In contrast, the relationships among dietary nutrients, host immunity and/or the gut microbiota may be perturbed in the context of IBD. Genetic predispositions and gut dysbiosis may affect the utilization of dietary nutrients. Moreover, the metabolism of nutrients in host cells and the gut microbiota may be altered by intestinal inflammation, thereby increasing or decreasing the demand for certain nutrients necessary for the maintenance of immune and microbial homeostasis. Herein, we review the current knowledge of the role dietary nutrients play in the development and the treatment of IBD, focusing on the interplay among dietary nutrients, the gut microbiota and host immune cells. We also discuss alterations in the nutritional metabolism of the gut microbiota and host cells in IBD that can influence the outcome of nutritional intervention. A better understanding of the diet-host-microbiota interactions may lead to new therapeutic approaches for the treatment of IBD.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Tina L Morhardt
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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Serkova NJ, Davis DM, Steiner J, Agarwal R. Quantitative NMR-Based Metabolomics on Tissue Biomarkers and Its Translation into In Vivo Magnetic Resonance Spectroscopy. Methods Mol Biol 2019; 1978:369-387. [PMID: 31119675 DOI: 10.1007/978-1-4939-9236-2_23] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an established analytical platform for analyzing metabolic profiles of cells, tissues, and body fluids. There are several advantages in introducing an NMR-based study design into metabolomics studies, including a fast and comprehensive detection, characterization, and quantification of dozens of endogenous metabolites in a single NMR spectrum. Quantitative proton 1H-NMR is the most useful NMR-based platform for metabolomics. The frozen tissues can be analyzed noninvasively using a high-resolution magic angle spinning (HR-MAS) 1H-NMR spectroscopy; or several extraction techniques can be applied to detect additional metabolites using a conventional liquid-based NMR technique. In this chapter, we report on tissue collection, handling, extraction methods, and 1H-NMR acquisition protocols developed in the past decades for a precise and quantitative NMR-metabolomics approach. The NMR acquisition protocols (both HR-MAS and conventional 1H-NMR spectroscopy) and spectral analysis steps are also presented. Since NMR can be applied "in vivo" using horizontal bore MRI scanners, several in vivo sequences for localized 1H-MRS (magnetic resonance spectroscopy) are presented which can be directly applied for noninvasive detection of brain metabolites.
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Affiliation(s)
- Natalie J Serkova
- Department of Radiology, School of Medicine, University of Colorado Denver, Aurora, CO, USA.
| | - Denise M Davis
- Department of Radiology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Jenna Steiner
- Department of Radiology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
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83
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Liu F, Wang M, Wang Y, Cao Y, Sun Z, Chen M, Tian X, Wan J, Huang C. Metabonomics Study on the Hepatoprotective Effect of Panax notoginseng Leaf Saponins Using UPLC/Q-TOF-MS Analysis. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2019; 47:559-575. [DOI: 10.1142/s0192415x19500290] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Alcohol liver disease is a major public health problem associated with lifestyle. Our recent study demonstrated that the roots of Panax notoginseng saponins (PNS) exert hepatoprotective effects against alcohol consumption. Considering that the leaves of Panax notoginseng saponins (LPNS) have similar chemical ingredients with PNS, increased attention should be given to the hepatoprotective effects of LPNS. In this study, a metabonomic approach based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS) was developed to evaluate the hepatoprotective effect of LPNS on alcoholic fatty liver and elucidate the interaction mechanisms. Results showed that the ethanol-induced metabolic perturbations were restored after treatment with LPNS. Furthermore, 12 potential biomarkers (11 upregulated and 1 downregulated) were identified by V-plot and orthogonal partial least square discriminant analysis. Changes in the levels of these metabolites indicated that glycerophospholipid and fatty acid metabolism were disturbed in alcoholic fatty liver mouse. Our findings demonstrated that the UHPLC–QTOF/MS-based metabonomic method may provide a useful means for exploring biomarkers involved in alcoholic fatty liver and elucidating the therapeutic effects of LPNS. This work also showed that the metabonomic approach is a powerful and promising tool for the evaluation of the efficacy of traditional Chinese medicine and elucidation of related mechanisms.
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Affiliation(s)
- Fang Liu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai Zhangjiang Hitech Park, Shanghai 201203, P. R. China
| | - Meng Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, P. R. China
| | - Yang Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, P. R. China
| | - Yiwei Cao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, P. R. China
| | - Zhaolin Sun
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai Zhangjiang Hitech Park, Shanghai 201203, P. R. China
| | - Mingcang Chen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai Zhangjiang Hitech Park, Shanghai 201203, P. R. China
| | - Xiaoting Tian
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai Zhangjiang Hitech Park, Shanghai 201203, P. R. China
| | - Jianbo Wan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, P. R. China
| | - Chenggang Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai Zhangjiang Hitech Park, Shanghai 201203, P. R. China
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84
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Chen S, Wang M, Yin L, Ren W, Bin P, Xia Y, Liu G, Yang H, Tan B, Yin Y. Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model. Food Funct 2018; 9:4143-4152. [PMID: 30042998 DOI: 10.1039/c8fo01025k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract and is strongly associated with intestinal immunity and the microbiome. Tryptophan (Trp) is an inflammatory inhibitor and modulator of the intestinal microflora. We explored the serum profile of amino acids and the effects of diet supplementation with Trp (1.0 g kg-1) on intestinal immunity and microbiota in the acetic acid-induced colitis mouse model. We analyzed the survival rate, colonic morphological parameters, profiles of serum amino acids, microbiota in colonic contents and the relative gene abundance of intestinal proinflammatory cytokines. Although the dietary Trp supplementation failed to improve the survival rate and ameliorate the morphological parameters of colon in mice with colitis, Trp modulated the general serum amino acid profile by reducing the amino acid profiles of threonine, methionine and proline, affected intestinal immunity by inhibiting the colonic expression of interleukin-22 and changed the microbiota by reducing the abundance of Candidatus, Clostridium and Coprococcus at the genus level. In conclusion, dietary Trp supplementation in a mouse model of colitis did not ameliorate the survival rate and morphological parameters of colon but did modulate the serum amino acid profiles, intestinal immunity and microbiota. These findings enhance our understanding of the roles of Trp in the metabolism of serum amino acids, intestinal immunity and microbiota.
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Affiliation(s)
- Shuai Chen
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, China.
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85
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Alghamdi A, Gerasimidis K, Blackburn G, Akinci D, Edwards C, Russell RK, Watson DG. Untargeted Metabolomics of Extracts from Faecal Samples Demonstrates Distinct Differences between Paediatric Crohn's Disease Patients and Healthy Controls but No Significant Changes Resulting from Exclusive Enteral Nutrition Treatment. Metabolites 2018; 8:E82. [PMID: 30467282 PMCID: PMC6315767 DOI: 10.3390/metabo8040082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/18/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Metabolomic profiling using high resolution mass spectrometry with hydrophilic interaction chromatography was applied to 11 faecal extracts from eleven healthy children and to 43 faecal extracts from eleven children undergoing exclusive enteral nutrition for the treatment of active Crohn's disease (CD) at timepoints before, during (15, 30, and 60 days), and after treatment. Differences between the control and CD samples were identified at each timepoint. An orthogonal partial least square-discriminant analysis (OPLS-DA) model identified eight metabolites that were normally distributed according to Q-Q plots. The OPLS-DA model was able to discriminate the CD samples from the controls at every timepoint, but the model was not able to differentiate the CD samples from one another at the different timepoints during treatment with exclusive enteral nutrition. The differentiated metabolites identified in the CD samples included tyrosine, an ornithine isomer, arachidonic acid, eicosatrienoic acid, docosatetraenoic acid, a sphingomyelin, a ceramide, and dimethylsphinganine. Despite successful treatment, underlying differences remained in the metabolome of the CD patients. These differences dominated the separation of the samples when multivariate methods were applied.
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Affiliation(s)
- Adel Alghamdi
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.
| | | | - Gavin Blackburn
- Glasgow Polyomics, Translational Cancer Research Centre, University of Glasgow Garscube Campus, Glasgow G61 1QH, UK.
| | - Didem Akinci
- Glasgow Polyomics, Translational Cancer Research Centre, University of Glasgow Garscube Campus, Glasgow G61 1QH, UK.
| | - Christine Edwards
- Glasgow Polyomics, Translational Cancer Research Centre, University of Glasgow Garscube Campus, Glasgow G61 1QH, UK.
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow G51 4TF, UK.
| | - David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.
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86
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Ramazzotti M, Stefanini I, Di Paola M, De Filippo C, Rizzetto L, Berná L, Dapporto L, Rivero D, Tocci N, Weil T, Lenucci MS, Lionetti P, Cavalieri D. Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut. Environ Microbiol 2018; 21:50-71. [PMID: 30246283 DOI: 10.1111/1462-2920.14422] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022]
Abstract
The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1715 combined CDSs from whole-genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain-specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodelling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut.
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Affiliation(s)
- Matteo Ramazzotti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Irene Stefanini
- Division of Biomedical Sciences, University of Warwick, Coventry, UK
| | - Monica Di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Pisa, Italy
| | - Lisa Rizzetto
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige (Trento), Italy
| | - Luisa Berná
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Damariz Rivero
- Department of Biology, University of Florence, Florence, Italy
| | - Noemi Tocci
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige (Trento), Italy
| | - Tobias Weil
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige (Trento), Italy
| | - Marcello S Lenucci
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (Di.S.Te.B.A.), Università del Salento, Lecce, Italy
| | - Paolo Lionetti
- Department of Neuroscience, Psychology, Drug Research and Child Health, Meyer Children Hospital, University of Florence, Florence, Italy
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87
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. Hochdurchsatz‐Metabolomik mit 1D‐NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P. Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Veronica Ghini
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Gaia Meoni
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Cristina Licari
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of Florence Largo Brambilla 3 Florence Italien
| | - Paola Turano
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| | - Claudio Luchinat
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
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88
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Sample preparation and recent trends in volatolomics for diagnosing gastrointestinal diseases. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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89
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Probert F, Walsh A, Jagielowicz M, Yeo T, Claridge TDW, Simmons A, Travis S, Anthony DC. Plasma Nuclear Magnetic Resonance Metabolomics Discriminates Between High and Low Endoscopic Activity and Predicts Progression in a Prospective Cohort of Patients With Ulcerative Colitis. J Crohns Colitis 2018; 12:1326-1337. [PMID: 30016408 PMCID: PMC6403054 DOI: 10.1093/ecco-jcc/jjy101] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS Endoscopic assessment of ulcerative colitis [UC] is one of the most accurate measures of disease activity, but frequent endoscopic investigations are disliked by patients and expensive for the healthcare system. A minimally invasive test that provides a surrogate measure of endoscopic activity is required. METHODS Plasma nuclear magnetic resonance [NMR] spectra from 40 patients with UC followed prospectively over 6 months were analysed with multivariate statistics. NMR metabolite profiles were compared with endoscopic [Ulcerative Colitis Endoscopic Index of Severity: UCEIS], histological [Nancy Index] and clinical [Simple Clinical Colitis Activity Index: SCCAI] severity indices, along with routine blood measurements. RESULTS A blinded principal component analysis spontaneously separated metabolite profiles of patients with low [≤3] and high [>3] UCEIS. Orthogonal partial least squares discrimination analysis identified low and high UCEIS metabolite profiles with an accuracy of 77 ± 5%. Plasma metabolites driving discrimination included decreases in lipoproteins and increases in isoleucine, valine, glucose and myo-inositol in high compared to low UCEIS. This same metabolite profile distinguished between low [Nancy 0-1] and high histological activity [Nancy 3-4] with a modest although significant accuracy [65 ± 6%] but was independent of SCCAI and all blood parameters measured. A different metabolite profile, dominated by changes in lysine, histidine, phenylalanine and tyrosine, distinguished between improvement in UCEIS [decrease ≥1] and worsening [increase ≥1] over 6 months with an accuracy of 74 ± 4%. CONCLUSION Plasma NMR metabolite analysis has the potential to provide a low-cost, minimally invasive technique that may be a surrogate for endoscopic assessment, with predictive capacity.
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Affiliation(s)
- Fay Probert
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Alissa Walsh
- Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marta Jagielowicz
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, and Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Tianrong Yeo
- Department of Pharmacology, University of Oxford, Oxford, UK,Department of Neurology, National Neuroscience Institute, Jalan Tan Tock Seng, Singapore
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, UK
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, and Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Simon Travis
- Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK,Corresponding author: Clinical: Simon Travis, Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK. ; Analysis and interpretation: Daniel Anthony, Department of Pharmacology, University of Oxford, Oxford, UK.
| | - Daniel C Anthony
- Department of Pharmacology, University of Oxford, Oxford, UK,Corresponding author: Clinical: Simon Travis, Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK. ; Analysis and interpretation: Daniel Anthony, Department of Pharmacology, University of Oxford, Oxford, UK.
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90
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Zhang XJ, Yuan ZW, Qu C, Yu XT, Huang T, Chen PV, Su ZR, Dou YX, Wu JZ, Zeng HF, Xie Y, Chen JN. Palmatine ameliorated murine colitis by suppressing tryptophan metabolism and regulating gut microbiota. Pharmacol Res 2018; 137:34-46. [PMID: 30243842 DOI: 10.1016/j.phrs.2018.09.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD), majorly include Crohn's disease (CD) and ulcerative colitis (UC), is chronic and relapsing inflammatory disorders of the gastrointestinal tract, which treatment options remain limited. Here we examined the therapeutic effects of an isoquinoline alkaloid, Palmatine (Pal), on mice experimental colitis induced by dextran sulfate sodium (DSS) and explored underlying mechanisms. Colitis was induced in BALB/c mice by administering 3% DSS in drinking water for 7 days. Pal (50 and 100 mg kg-1) and the positive drug Sulfasalazine (SASP, 200 mg kg-1) were orally administered for 7 days. Disease activity index (DAI) was evaluated on day 8, and colonic tissues were collected for biochemistry analysis. The fecal microbiota was characterized by high-throughput Illumina MiSeq sequencing. And plasma metabolic changes were detected by UPLC-MS. Our results showed that Pal treatment significantly reduced DAI scores and ameliorated colonic injury in mice with DSS-induced colitis. Mucosal integrity was improved and cell apoptosis was inhibited. Moreover, gut microbiota analysis showed that mice received Pal-treatment have higher relative abundance of Bacteroidetes and Firmicutes, but reduced amount of Proteobacteria. Moreover, Pal not only suppressed tryptophan catabolism in plasma, but also decreased the protein expression of indoleamine 2,3-dioxygenase 1 (IDO-1, the rate-limiting enzyme of tryptophan catabolism) in colon tissue. This is consolidated by molecular docking, which suggested that Pal is a potent IDO-1 inhibitor. Taken together, our findings demonstrate that Pal ameliorated DSS-induced colitis by mitigating colonic injury, preventing gut microbiota dysbiosis, and regulating tryptophan catabolism, which indicated that Pal has great therapeutic potential for colitis.
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Affiliation(s)
- Xiao-Jun Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China.
| | - Zhong-Wen Yuan
- State Key Laboratory for Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau.
| | - Chang Qu
- Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China.
| | - Xiu-Ting Yu
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, PR China.
| | - Tao Huang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| | - Ping Vicky Chen
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
| | - Zi-Ren Su
- Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China.
| | - Yao-Xing Dou
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, PR China.
| | - Jia-Zhen Wu
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, PR China.
| | - Hui-Fang Zeng
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, PR China.
| | - Ying Xie
- State Key Laboratory for Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau.
| | - Jian-Nan Chen
- Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China.
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91
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Metabolomics in chronic kidney disease: Strategies for extended metabolome coverage. J Pharm Biomed Anal 2018; 161:313-325. [PMID: 30195171 DOI: 10.1016/j.jpba.2018.08.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/16/2022]
Abstract
Chronic kidney disease (CKD) is becoming a major public health issue as prevalence is increasing worldwide. It also represents a major challenge for the identification of new early biomarkers, understanding of biochemical mechanisms, patient monitoring and prognosis. Each metabolite contained in a biofluid or tissue may play a role as a signal or as a driver in the development or progression of the pathology. Therefore, metabolomics is a highly valuable approach in this clinical context. It aims to provide a representative picture of a biological system, making exhaustive metabolite coverage crucial. Two aspects can be considered: analytical and biological coverage. From an analytical point of view, monitoring all metabolites within one run is currently impossible. Multiple analytical techniques providing orthogonal information should be carried out in parallel for coverage improvement. The biological aspect of metabolome coverage can be enhanced by using multiple biofluids or tissues for in-depth biological investigation, as the analysis of a single sample type is generally insufficient for whole organism extrapolation. Hence, recording of signals from multiple sample types and different analytical platforms generates massive and complex datasets so that chemometric tools, including data fusion approaches and multi-block analysis, are key tools for extracting biological information and for discovery of relevant biomarkers. This review presents the recent developments in the field of metabolomic analysis, from sampling and analytical strategies to chemometric tools, dedicated to the generation and handling of multiple complementary metabolomic datasets enabling extended metabolite coverage to improve our biological knowledge of CKD.
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92
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Miyake M, Fujishima M, Nakai D. Inhibitory Potency of Marketed Drugs for Ulcerative Colitis and Crohn's Disease on PEPT1. Biol Pharm Bull 2018; 40:1572-1575. [PMID: 28867741 DOI: 10.1248/bpb.b17-00181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigate the inhibitory effect of marketed drugs for treatment of inflammatory bowel disease (IBD) such as ulcerative colitis (UC) and Crohn's disease (CD) on the uptake transporters of peptide transporter 1 (PEPT1), which are up-regulated under the inflamed condition. The uptake transport of glycylsarcosine, a typical substrate for PEPT1, was reduced to 60% only by 5-aminosalicylate at the clinically relevant concentration among tested marketed drugs in PEPT1 transfected HEK293 cell lines. These findings suggest that the inhibition of PEPT1, which were up-regulated in inflamed or non-inflamed site on UC and CD patients, contribute to the clinical effect of commercially available drugs for IBD patients through the inhibition of uptake of antigenic proinflammatory oligopeptides such as formyl-methionine (Met)-leucine (Leu)-phenylalanine (Phe) via PEPT1.
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Affiliation(s)
- Masateru Miyake
- Department of Pharmacy, Uppsala University.,BA Project, Formulation Research Institute, Otsuka Pharmaceutical Co., Ltd
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93
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Marlicz W, Skonieczna-Żydecka K, Dabos KJ, Łoniewski I, Koulaouzidis A. Emerging concepts in non-invasive monitoring of Crohn's disease. Therap Adv Gastroenterol 2018; 11:1756284818769076. [PMID: 29707039 PMCID: PMC5912292 DOI: 10.1177/1756284818769076] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is an umbrella term for Crohn's disease (CD) and ulcerative colitis (UC). In light of evolving epidemiology of CD, its clinical management is still complex and remains a challenge for contemporary physicians. With the advent of new diagnostic and treatment paradigms, there is a growing need for new biomarkers to guide decision-making, differential diagnosis, disease activity monitoring, as well as prognosis. However, both clinical and endoscopic scoring systems, widely utilized for disease monitoring and prognosis, have drawbacks and limitations. In recent years, biochemical peptides have become available for IBD monitoring and more frequently used as surrogate markers of gut inflammation. Emerging concepts that revolve around molecular, stem cell, epigenetic, microbial or metabolomic pathways associated with vascular and epithelial gut barrier could lead to development of new CD biomarkers. Measurement of cell-derived microvesicles (MVs) in the blood of IBD patients is another emerging concept helpful in future disease management. In this review, we discuss novel concepts of non-invasive biomarkers, which may become useful in monitoring of CD activity and prognosis. We discuss metabolomics as a new powerful tool for clinicians to guide differential IBD diagnosis. In the coming years, new developments of prognostic tools are expected, aiming for breakthroughs in the management of patients with CD.
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Affiliation(s)
- Wojciech Marlicz
- Department of Gastroenterology, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | | | | | - Igor Łoniewski
- Department of Biochemistry and Human Nutrition, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. K., Szczecin, Poland
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94
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Severity of allergic rhinitis assessed by using urine metabolomic profiling: Proof of concept. J Allergy Clin Immunol 2018; 142:687-689.e6. [PMID: 29678748 DOI: 10.1016/j.jaci.2018.02.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/09/2018] [Accepted: 02/21/2018] [Indexed: 12/25/2022]
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95
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Leng J, Proudman C, Darby A, Blow F, Townsend N, Miller A, Swann J. Exploration of the Fecal Microbiota and Biomarker Discovery in Equine Grass Sickness. J Proteome Res 2018; 17:1120-1128. [DOI: 10.1021/acs.jproteome.7b00784] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joy Leng
- School
of Veterinary Medicine, Vet School Main Building, Daphne Jackson Road, University of Surrey, Guildford, Surrey GU2 7AL, United Kingdom
| | - Chris Proudman
- School
of Veterinary Medicine, Vet School Main Building, Daphne Jackson Road, University of Surrey, Guildford, Surrey GU2 7AL, United Kingdom
| | - Alistair Darby
- School
of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Frances Blow
- School
of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Neil Townsend
- Philip
Leverhulme Equine Hospital, University of Liverpool, Leahurst Campus,
Chester High Road, Wirral CH64 7TE, United Kingdom
| | - Andrew Miller
- Philip
Leverhulme Equine Hospital, University of Liverpool, Leahurst Campus,
Chester High Road, Wirral CH64 7TE, United Kingdom
| | - Jonathan Swann
- Division
of Computational and Systems Medicine, Department of Surgery and Cancer,
Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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96
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Nair AT, Ramachandran V, Joghee NM, Antony S, Ramalingam G. Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson's Disease: A Critical Review. J Neurogastroenterol Motil 2018; 24:30-42. [PMID: 29291606 PMCID: PMC5753901 DOI: 10.5056/jnm17105] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/08/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
Recent investigations suggest that gut microbiota affects the brain activity through the microbiota-gut-brain axis under both physiological and pathological disease conditions like Parkinson's disease. Further dopamine synthesis in the brain is induced by dopamine producing enzymes that are controlled by gut microbiota via the microbiota-gut-brain axis. Also alpha synuclein deposition and the associated neurodegeneration in the enteric nervous system that increase intestinal permeability, oxidative stress, and local inflammation, accounts for constipation in Parkinson's disease patients. The trigger that causes blood brain barrier leakage, immune cell activation and inflammation, and ultimately neuroinflammation in the central nervous system is believed to be due to the chronic low-grade inflammation in the gut. The non-motor symptoms that appear years before motor symptoms could be reliable early biomarkers, if they could be correlated with the established and reliable neuroimaging techniques or behavioral indices. The future directions should therefore, focus on the exploration of newer investigational techniques to identify these reliable early biomarkers and define the specific gut microbes that contribute to the development of Parkinson's disease. This ultimately should pave the way to safer and novel therapeutic approaches that avoid the complications of the drugs delivered today to the brain of Parkinson's disease patients.
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Affiliation(s)
- Arun T Nair
- Department of Pharmacology, JSS College of Pharmacy (JSS Academy of Higher Education and Research, Mysuru), Ootacamund, Tamilnadu,
India
| | - Vadivelan Ramachandran
- Department of Pharmacology, JSS College of Pharmacy (JSS Academy of Higher Education and Research, Mysuru), Ootacamund, Tamilnadu,
India
- Correspondence: Vadivelan Ramachandran, PhD, Department of Pharmacology, JSS College of Pharmacy ((JSS Academy of Higher Education and Research, Mysuru), Ootacamund, Tamilnadu 643001, India Tel: +91-9047539532, Fax: +91-423-2442937,
| | - Nanjan M Joghee
- JSS College of Pharmacy (JSS Academy of Higher Education and Research, Mysuru), Ootacamund, Tamilnadu,
India
| | - Shanish Antony
- Department of Pharmacology, Government Medical College, Kottayam, Kerala,
India
| | - Gopalakrishnan Ramalingam
- Department of Pharmacology, JSS College of Pharmacy (JSS Academy of Higher Education and Research, Mysuru), Ootacamund, Tamilnadu,
India
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97
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Yang C, Lai W, Zhou J, Zheng X, Cai Y, Yang W, Xie S, Gao Y, Du C. Betaine Ameliorates Experimental Autoimmune Encephalomyelitis by Inhibiting Dendritic Cell-Derived IL-6 Production and Th17 Differentiation. THE JOURNAL OF IMMUNOLOGY 2018; 200:1316-1324. [PMID: 29330324 DOI: 10.4049/jimmunol.1700920] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/15/2017] [Indexed: 12/14/2022]
Abstract
IL-17-secreting T cells (Th17 cells) play a pathogenic role in multiple autoimmune diseases, including multiple sclerosis (MS), and dendritic cell (DC)-derived cytokines play pivotal roles in promoting the differentiation of naive CD4+ T cells into Th cell subsets (Th1 and Th17). Therefore, small molecules blocking the key cytokines produced by DCs will be beneficial in MS. In this article, we report that betaine treatment ameliorates MS pathogenesis by inhibiting DC-derived IL-6 production and Th17 differentiation. Using experimental autoimmune encephalomyelitis, a widely used mouse model of MS, we found that, compared with the vehicle-treated group, betaine-treated mice exhibited less severe experimental autoimmune encephalomyelitis symptoms, including lower clinical scores, reduced leukocyte infiltration, and less extensive demyelination in the CNS. Moreover, a significantly lower percentage of Th17 cells, one of the major pathogenic effector cells in MS progression, was observed in the peripheral immune system and in the CNS. Interestingly, in the in vitro Th17-differentiation assay, no significant change in Th17 cells was observed between the vehicle- and betaine-treated groups, whereas in the in vitro DC culture experiment, betaine treatment significantly decreased DC-derived IL-6 production. In the DC-T cell coculture experiment, a significantly decreased Th17 differentiation was observed upon betaine treatment. All of these data demonstrated that betaine inhibited Th17 differentiation indirectly by reducing IL-6 production by DCs. In brief, our findings demonstrated the pivotal roles of betaine in modulating MS pathogenesis and suggested that it may serve as a potential novel drug candidate for the treatment of MS.
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Affiliation(s)
- Cuixia Yang
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Weiming Lai
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jinfeng Zhou
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xinyuan Zheng
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yingying Cai
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Wanjie Yang
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Sirong Xie
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuan Gao
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Changsheng Du
- Putuo District People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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98
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Scoville EA, Allaman MM, Brown CT, Motley AK, Horst SN, Williams CS, Koyama T, Zhao Z, Adams DW, Beaulieu DB, Schwartz DA, Wilson KT, Coburn LA. Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn's Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling. Metabolomics 2018; 14:17. [PMID: 29681789 PMCID: PMC5907923 DOI: 10.1007/s11306-017-1311-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. OBJECTIVES The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn's disease (CD), and non- IBD subjects. METHODS Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS). RESULTS In total, 671 metabolites were identified. Comparing IBD and control subjects revealed 173 significantly altered metabolites (27 increased and 146 decreased). The majority of the alterations occurred in lipid-, amino acid-, and energy-related metabolites. Comparing only CD and control subjects revealed 286 significantly altered metabolites (54 increased and 232 decreased), whereas comparing UC and control subjects revealed only 5 significantly altered metabolites (all decreased). Hierarchal clustering using significant metabolites separated CD from UC and control subjects. CONCLUSIONS We demonstrate that a number of lipid-, amino acid-, and tricarboxylic acid (TCA) cycle- related metabolites were significantly altered in IBD patients, more specifically in CD. Therefore, alterations in lipid and amino acid metabolism and energy homeostasis may play a key role in the pathogenesis of CD.
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Affiliation(s)
- Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - Caroline T Brown
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - Amy K Motley
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - Sara N Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - Christopher S Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Tatsuki Koyama
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zhiguo Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dawn W Adams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Dawn B Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - David A Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Mucosal Inflammation and Cancer, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232, USA.
- Vanderbilt Center for Mucosal Inflammation and Cancer, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
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99
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de Souza HSP, Fiocchi C, Iliopoulos D. The IBD interactome: an integrated view of aetiology, pathogenesis and therapy. Nat Rev Gastroenterol Hepatol 2017; 14:739-749. [PMID: 28831186 DOI: 10.1038/nrgastro.2017.110] [Citation(s) in RCA: 274] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules. To define the IBD interactome, new concepts and tools are needed to implement a systems approach; an unbiased data-driven integration strategy that reveals key players of the system, pinpoints the central drivers of inflammation and enables development of targeted therapies. Powerful bioinformatics tools able to query and integrate multiple -omes are available, enabling the integration of genomic, epigenomic, transcriptomic, proteomic, metabolomic and microbiome information to build a comprehensive molecular map of IBD. This approach will enable identification of IBD molecular subtypes, correlations with clinical phenotypes and elucidation of the central hubs of the IBD interactome that will aid discovery of compounds that can specifically target the hubs that control the disease.
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Affiliation(s)
- Heitor S P de Souza
- Department of Gastroenterology & Multidisciplinary Research Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro 21941-913, Brazil
| | - Claudio Fiocchi
- Department of Pathobiology, Lerner Research Institute, Department of Gastroenterology and Hepatology, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Dimitrios Iliopoulos
- Center for Systems Biomedicine, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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100
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Bjerrum JT, Steenholdt C, Ainsworth M, Nielsen OH, Reed MA, Atkins K, Günther UL, Hao F, Wang Y. Metabonomics uncovers a reversible proatherogenic lipid profile during infliximab therapy of inflammatory bowel disease. BMC Med 2017; 15:184. [PMID: 29032767 PMCID: PMC5641999 DOI: 10.1186/s12916-017-0949-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/29/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND One-third of inflammatory bowel disease (IBD) patients show no response to infliximab (IFX) induction therapy, and approximately half of patients responding become unresponsive over time. Thus, identification of potential treatment response biomarkers are of great clinical significance. This study employs spectroscopy-based metabolic profiling of serum from patients with IBD treated with IFX and healthy subjects (1) to substantiate the use of spectroscopy as a semi-invasive diagnostic tool, (2) to identify potential biomarkers of treatment response and (3) to characterise the metabolic changes during management of patients with tumour necrosis factor-α inhibitors. METHODS Successive serum samples collected during IFX induction treatment (weeks 0, 2, 6 and 14) from 87 IBD patients and 37 controls were analysed by 1H nuclear magnetic resonance (NMR) spectroscopy. Data were analysed with principal components analysis and orthogonal projection to latent structures discriminant analysis using SIMCA-P+ v12 and MATLAB. RESULTS Metabolic profiles were significantly different between active ulcerative colitis and controls, active Crohn's disease and controls, and quiescent Crohn's disease and controls. Metabolites holding differential power belonged primarily to lipids and phospholipids with proatherogenic characteristics and metabolites in the pyruvate metabolism, suggestive of an intense inflammation-driven energy demand. IBD patients not responding to IFX were identified as a potentially distinct group based on their metabolic profile, although no applicable response biomarkers could be singled out in the current setting. CONCLUSION 1H NMR spectroscopy of serum samples is a powerful semi-invasive diagnostic tool in flaring IBD. With its use, we provide unique insights into the metabolic changes taking place during induction treatment with IFX. Of distinct clinical relevance is the identification of a reversible proatherogenic lipid profile in IBD patients with active disease, which partially explains the increased risk of cardiovascular disease associated with IBD.
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Affiliation(s)
- Jacob Tveiten Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark.
| | - Casper Steenholdt
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Mark Ainsworth
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Michelle Ac Reed
- HWB-NMR, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Karen Atkins
- HWB-NMR, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ulrich Leonhard Günther
- HWB-NMR, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Fuhua Hao
- 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, The Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - 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, The Chinese Academy of Sciences, Wuhan, People's Republic of China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
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