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Alexander JL, Wyatt NJ, Camuzeaux S, Chekmeneva E, Jimenez B, Sands CJ, Fuller H, Takis P, Ahmad T, Doyle JA, Hart A, Irving PM, Kennedy NA, Lees CW, Lindsay JO, McIntyre RE, Parkes M, Prescott NJ, Raine T, Satsangi J, Speight RA, Jostins-Dean L, Powell N, Marchesi JR, Stewart CJ, Lamb CA. Considerations for peripheral blood transport and storage during large-scale multicentre metabolome research. Gut 2024; 73:379-383. [PMID: 36754608 PMCID: PMC10850673 DOI: 10.1136/gutjnl-2022-329297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023]
Affiliation(s)
- James L Alexander
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Nicola J Wyatt
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Stephane Camuzeaux
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Elena Chekmeneva
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Beatriz Jimenez
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Caroline J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Hannah Fuller
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Panteleimon Takis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Tariq Ahmad
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, Devon, UK
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jennifer A Doyle
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ailsa Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Gastroenterology, St Mark's Hospital and Academic Institute, London, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' Hospitals NHS Trust, London, UK
- School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nicholas A Kennedy
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, Devon, UK
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Charlie W Lees
- Edinburgh IBD Unit, Western General Hospital, Edinburgh, UK
- Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - James O Lindsay
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine, Queen Mary University of London, London, UK
- Department of Gastroenterology, Barts Health NHS Trust, London, UK
| | - Rebecca E McIntyre
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Natalie J Prescott
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Tim Raine
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Richard Alexander Speight
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Luke Jostins-Dean
- Kennedy Institute of Rheumatology, Oxford University, Oxford, Oxfordshire, UK
| | - Nick Powell
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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Kragsnaes MS, Miguens Blanco J, Mullish BH, Serrano‐Contreras JI, Kjeldsen J, Horn HC, Pedersen JK, Munk HL, Nilsson AC, Salam A, Lewis MR, Chekmeneva E, Kristiansen K, Marchesi JR, Ellingsen T. Small Intestinal Permeability and Metabolomic Profiles in Feces and Plasma Associate With Clinical Response in Patients With Active Psoriatic Arthritis Participating in a Fecal Microbiota Transplantation Trial: Exploratory Findings From the FLORA Trial. ACR Open Rheumatol 2023; 5:583-593. [PMID: 37736702 PMCID: PMC10642255 DOI: 10.1002/acr2.11604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023] Open
Abstract
OBJECTIVE We investigated intestinal permeability and fecal, plasma, and urine metabolomic profiles in methotrexate-treated active psoriatic arthritis (PsA) and how this related to clinical response following one sham or fecal microbiota transplantation (FMT). METHODS This exploratory study is based on the FLORA trial cohort, in which 31 patients with moderate-to-high peripheral PsA disease activity, despite at least 3 months of methotrexate-treatment, were included in a 26-week, double-blind, 1:1 randomized, sham-controlled trial. Participants were randomly allocated to receive either one healthy donor FMT (n = 15) or sham (n = 16) via gastroscopy. The primary trial end point was the proportion of treatment failures through 26 weeks. We performed a lactulose-to-mannitol ratio (LMR) test at baseline (n = 31) and at week 26 (n = 26) to assess small intestinal permeability. Metabolomic profiles in fecal, plasma, and urine samples collected at baseline, weeks 4, 12, and 26 were measured using 1 H Nuclear Magnetic Resonance. RESULTS Trial failures (n = 7) had significantly higher LMR compared with responders (n = 19) at week 26 (0.027 [0.017-0.33]) vs. 0.012 [0-0.064], P = 0.013), indicating increased intestinal permeability. Multivariate analysis revealed a significant model for responders (n = 19) versus failures (n = 12) at all time points based on their fecal (P < 0.0001) and plasma (P = 0.005) metabolomic profiles, whereas urine metabolomic profiles did not differ between groups (P = 1). Fecal N-acetyl glycoprotein GlycA correlated with Health Assessment Questionnaire Disability Index (coefficient = 0.50; P = 0.03) and fecal propionate correlated with American College of Rheumatology 20 response at week 26 (coefficient = 27, P = 0.02). CONCLUSION Intestinal permeability and fecal and plasma metabolomic profiles of patients with PsA were associated with the primary clinical trial end point, failure versus responder.
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Affiliation(s)
| | | | - Benjamin H. Mullish
- Imperial College London and St. Mary's Hospital, Imperial College Healthcare National Health Service TrustLondonUK
| | | | - Jens Kjeldsen
- Odense University Hospital and University of Southern DenmarkOdenseDenmark
| | | | | | | | | | - Ash Salam
- Imperial College London, Hammersmith Hospital CampusLondonUK
| | | | | | - Karsten Kristiansen
- University of Copenhagen, Copenhagen, Denmark, and Institute of Metagenomics, Qingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
| | | | - Torkell Ellingsen
- Odense University Hospital and University of Southern DenmarkOdenseDenmark
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3
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Alhamad S, Elmasry Y, Uwagboe I, Chekmeneva E, Sands C, Cooper BW, Camuzeaux S, Salam A, Parsons M. B7-H3 Associates with IMPDH2 and Regulates Cancer Cell Survival. Cancers (Basel) 2023; 15:3530. [PMID: 37444640 DOI: 10.3390/cancers15133530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Lung cancer is one of the most common cancers worldwide, and despite improvements in treatment regimens, patient prognosis remains poor. Lung adenocarcinomas develop from the lung epithelia and understanding how specific genetic and environmental factors lead to oncogenic transformation in these cells is of great importance to define the pathways that contribute to tumorigenesis. The recent rise in the use of immunotherapy to treat different cancers has prompted the exploration of immune modulators in tumour cells that may provide new targets to manipulate this process. Of these, the B7 family of cell surface receptors, which includes PD-1, is of particular interest due to its role in modulating immune cell responses within the tumour microenvironment. B7-H3 (CD276) is one family member that is upregulated in many cancer types and suggested to contribute to tumour-immune interactions. However, the function and ligand(s) for this receptor in normal lung epithelia and the mechanisms through which the overexpression of B7-H3 regulate cancer progression in the absence of immune cell interactions remain unclear. Here, we present evidence that B7-H3 is associated with one of the key rate-limiting metabolic enzymes IMPDH2, and the localisation of this complex is altered in human lung cancer cells that express high levels of B7-H3. Mechanistically, the IMPDH2:B7-H3 complex provides a protective role in cancer cells to escape oxidative stress triggered by chemotherapy, thus leading to cell survival. We further demonstrate that the loss of B7-H3 in cancer cells has no effect on growth or migration in 2D but promotes the expansion of 3D spheroids in an IMPDH2-dependent manner. These findings provide new insights into the B7-H3 function in the metabolic homeostasis of normal and transformed lung cancer cells, and whilst this molecule remains an interesting target for immunotherapy, these findings caution against the use of anti-B7-H3 therapies in certain clinical settings.
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Affiliation(s)
- Salwa Alhamad
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guys Campus, New Hunts House, London SE1 1UL, UK
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Yassmin Elmasry
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guys Campus, New Hunts House, London SE1 1UL, UK
| | - Isabel Uwagboe
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guys Campus, New Hunts House, London SE1 1UL, UK
| | - Elena Chekmeneva
- National Phenome Centre, Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, IRDB Building, 5th Floor, Du Cane Road, London W12 0NN, UK
| | - Caroline Sands
- National Phenome Centre, Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, IRDB Building, 5th Floor, Du Cane Road, London W12 0NN, UK
| | - Benjamin W Cooper
- National Phenome Centre, Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, IRDB Building, 5th Floor, Du Cane Road, London W12 0NN, UK
| | - Stephane Camuzeaux
- National Phenome Centre, Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, IRDB Building, 5th Floor, Du Cane Road, London W12 0NN, UK
| | - Ash Salam
- National Phenome Centre, Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, IRDB Building, 5th Floor, Du Cane Road, London W12 0NN, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guys Campus, New Hunts House, London SE1 1UL, UK
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4
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de Jonge NF, Louwen JJR, Chekmeneva E, Camuzeaux S, Vermeir FJ, Jansen RS, Huber F, van der Hooft JJJ. MS2Query: reliable and scalable MS 2 mass spectra-based analogue search. Nat Commun 2023; 14:1752. [PMID: 36990978 PMCID: PMC10060387 DOI: 10.1038/s41467-023-37446-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Metabolomics-driven discoveries of biological samples remain hampered by the grand challenge of metabolite annotation and identification. Only few metabolites have an annotated spectrum in spectral libraries; hence, searching only for exact library matches generally returns a few hits. An attractive alternative is searching for so-called analogues as a starting point for structural annotations; analogues are library molecules which are not exact matches but display a high chemical similarity. However, current analogue search implementations are not yet very reliable and relatively slow. Here, we present MS2Query, a machine learning-based tool that integrates mass spectral embedding-based chemical similarity predictors (Spec2Vec and MS2Deepscore) as well as detected precursor masses to rank potential analogues and exact matches. Benchmarking MS2Query on reference mass spectra and experimental case studies demonstrate improved reliability and scalability. Thereby, MS2Query offers exciting opportunities to further increase the annotation rate of metabolomics profiles of complex metabolite mixtures and to discover new biology.
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Affiliation(s)
- Niek F de Jonge
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Elena Chekmeneva
- National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Stephane Camuzeaux
- National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Femke J Vermeir
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525ED, Nijmegen, the Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525ED, Nijmegen, the Netherlands
| | - Florian Huber
- Centre for Digitalization and Digitality (ZDD), University of Applied Sciences Düsseldorf, Düsseldorf, Germany.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa.
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5
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Augustin A, Guennec AL, Umamahesan C, Kendler‐Rhodes A, Tucker RM, Chekmeneva E, Takis P, Lewis M, Balasubramanian K, DeSouza N, Mullish BH, Taylor D, Ryan S, Whelan K, Ma Y, Ibrahim MAA, Bjarnason I, Hayee BH, Charlett A, Dobbs SM, Dobbs RJ, Weller C. Faecal metabolite deficit, gut inflammation and diet in Parkinson's disease: Integrative analysis indicates inflammatory response syndrome. Clin Transl Med 2023; 13:e1152. [PMID: 36588088 PMCID: PMC9806009 DOI: 10.1002/ctm2.1152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/16/2022] [Accepted: 12/08/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Gut-brain axis is widely implicated in the pathophysiology of Parkinson's disease (PD). We take an integrated approach to considering the gut as a target for disease-modifying intervention, using continuous measurements of disease facets irrespective of diagnostic divide. METHODS We characterised 77 participants with diagnosed-PD, 113 without, by dietary/exogenous substance intake, faecal metabolome, intestinal inflammation, serum cytokines/chemokines, clinical phenotype including colonic transit time. Complete-linkage hierarchical cluster analysis of metabolites discriminant for PD-status was performed. RESULTS Longer colonic transit was linked to deficits in faecal short-chain-fatty acids outside PD, to a 'tryptophan-containing metabolite cluster' overall. Phenotypic cluster analysis aggregated colonic transit with brady/hypokinesia, tremor, sleep disorder and dysosmia, each individually associated with tryptophan-cluster deficit. Overall, a faster pulse was associated with deficits in a metabolite cluster including benzoic acid and an imidazole-ring compound (anti-fungals) and vitamin B3 (anti-inflammatory) and with higher serum CCL20 (chemotactic for lymphocytes/dendritic cells towards mucosal epithelium). The faster pulse in PD was irrespective of postural hypotension. The benzoic acid-cluster deficit was linked to (well-recognised) lower caffeine and alcohol intakes, tryptophan-cluster deficit to higher maltose intake. Free-sugar intake was increased in PD, maltose intake being 63% higher (p = .001). Faecal calprotectin was 44% (95% CI 5%, 98%) greater in PD [p = .001, adjusted for proton-pump inhibitors (p = .001)], with 16% of PD-probands exceeding a cut-point for clinically significant inflammation compatible with inflammatory bowel disease. Higher maltose intake was associated with exceeding this calprotectin cut-point. CONCLUSIONS Emerging picture is of (i) clinical phenotype being described by deficits in microbial metabolites essential to gut health; (ii) intestinal inflammation; (iii) a systemic inflammatory response syndrome.
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Affiliation(s)
- Aisha Augustin
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- The Maudsley HospitalLondonUK
| | | | - Chianna Umamahesan
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- The Maudsley HospitalLondonUK
| | | | - Rosalind M. Tucker
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- The Maudsley HospitalLondonUK
| | - Elena Chekmeneva
- National Phenome CentreImperial College LondonLondonUK
- Section of Bioanalytical ChemistryImperial College LondonLondonUK
| | - Panteleimon Takis
- National Phenome CentreImperial College LondonLondonUK
- Section of Bioanalytical ChemistryImperial College LondonLondonUK
| | - Matthew Lewis
- National Phenome CentreImperial College LondonLondonUK
- Section of Bioanalytical ChemistryImperial College LondonLondonUK
| | | | | | - Benjamin H Mullish
- Department of MetabolismDigestion and ReproductionImperial College, LondonUK
| | - David Taylor
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- The Maudsley HospitalLondonUK
| | | | - Kevin Whelan
- Nutritional SciencesKing's College LondonLondonUK
| | - Yun Ma
- Institute of Liver StudiesKing's College HospitalLondonUK
| | | | | | | | - André Charlett
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- Statistics, Modelling and EconomicsUK Health Security AgencyLondonUK
| | - Sylvia M. Dobbs
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- GastroenterologyKing's College HospitalLondonUK
| | - R. John Dobbs
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
- GastroenterologyKing's College HospitalLondonUK
| | - Clive Weller
- Institute of Pharmaceutical ScienceKing's College LondonLondonUK
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6
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Mullish BH, Martinez-Gili L, Chekmeneva E, Correia GDS, Lewis MR, Horneffer-Van Der Sluis V, Roberts LA, McDonald JAK, Pechlivanis A, Walters JRF, McClure EL, Marchesi JR, Allegretti JR. Assessing the clinical value of faecal bile acid profiling to predict recurrence in primary Clostridioides difficile infection. Aliment Pharmacol Ther 2022; 56:1556-1569. [PMID: 36250604 DOI: 10.1111/apt.17247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/30/2022] [Accepted: 09/26/2022] [Indexed: 01/30/2023]
Abstract
BACKGROUND Factors influencing recurrence risk in primary Clostridioides difficile infection (CDI) are poorly understood, and tools predicting recurrence are lacking. Perturbations in bile acids (BAs) contribute to CDI pathogenesis and may be relevant to primary disease prognosis. AIMS To define stool BA dynamics in patients with primary CDI and to explore signatures predicting recurrence METHODS: Weekly stool samples were collected from patients with primary CDI from the last day of anti-CDI therapy until recurrence or, otherwise, through 8 weeks post-completion. Ultra-high performance liquid chromatography-mass spectrometry was used to profile BAs. Stool bile salt hydrolase (BSH) activity was measured to determine primary BA bacterial deconjugation capacity. Multivariate and univariate models were used to define differential BA trajectories in patients with recurrence versus those without, and to assess faecal BAs as predictive markers for recurrence. RESULTS Twenty (36%) of 56 patients (median age: 57, 64% male) had recurrence; 80% of recurrences occurred within the first 9 days post-antibiotic treatment. Principal component analysis of stool BA profiles demonstrated clustering by recurrence status and post-treatment timepoint. Longitudinal faecal BA trajectories showed recovery of secondary BAs and their derivatives only in patients without recurrence. BSH activity increased over time only among non-relapsing patients (β = 0.056; likelihood ratio test p = 0.018). A joint longitudinal-survival model identified five stool BAs with area under the receiver operating characteristic curve >0.73 for predicting recurrence within 9 days post-CDI treatment. CONCLUSIONS Gut BA metabolism dynamics differ in primary CDI patients between those developing recurrence and those who do not. Individual BAs show promise as potential novel biomarkers to predict CDI recurrence.
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Affiliation(s)
- Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK.,Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Laura Martinez-Gili
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK.,Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Elena Chekmeneva
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, National Phenome Centre, IRDB Building, Hammersmith House Campus, Imperial College London, London, UK.,Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Gonçalo D S Correia
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, National Phenome Centre, IRDB Building, Hammersmith House Campus, Imperial College London, London, UK.,Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Matthew R Lewis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, National Phenome Centre, IRDB Building, Hammersmith House Campus, Imperial College London, London, UK.,Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Verena Horneffer-Van Der Sluis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, National Phenome Centre, IRDB Building, Hammersmith House Campus, Imperial College London, London, UK.,Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,Department for Diagnostics, Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Lauren A Roberts
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Julie A K McDonald
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Alexandros Pechlivanis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Thessaloniki, Greece
| | - Julian R F Walters
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK.,Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Emma L McClure
- Division of Gastroenterology, Hepatology, and Endoscopy, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Jessica R Allegretti
- Division of Gastroenterology, Hepatology, and Endoscopy, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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7
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Gadgil MD, Kanaya AM, Sands C, Chekmeneva E, Lewis MR, Kandula NR, Herrington DM. Diet Patterns Are Associated with Circulating Metabolites and Lipid Profiles of South Asians in the United States. J Nutr 2022; 152:2358-2366. [PMID: 36774102 PMCID: PMC10157813 DOI: 10.1093/jn/nxac191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/03/2022] [Accepted: 08/18/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND South Asians are at higher risk for cardiometabolic disease than many other racial/ethnic minority groups. Diet patterns in US South Asians have unique components associated with cardiometabolic disease. OBJECTIVES We aimed to characterize the metabolites associated with 3 representative diet patterns. METHODS We included 722 participants in the Mediators of Atherosclerosis in South Asians Living in America (MASALA) cohort study aged 40-84 y without known cardiovascular disease. Fasting serum specimens and diet and demographic questionnaires were collected at baseline and diet patterns previously generated through principal components analysis. LC-MS-based untargeted metabolomic and lipidomic analysis was conducted with targeted integration of known metabolite and lipid signals. Linear regression models of diet pattern factor score and log-transformed metabolites adjusted for age, sex, caloric intake, and BMI and adjusted for multiple comparisons were performed, followed by elastic net linear regression of significant metabolites. RESULTS There were 443 metabolites of known identity extracted from the profiling data. The "animal protein" diet pattern was associated with 61 metabolites and lipids, including glycerophospholipids phosphatidylethanolamine PE(O-16:1/20:4) and/or PE(P-16:0/20:4) (β: 0.13; 95% CI: 0.11, 0.14) and N-acyl phosphatidylethanolamines (NAPEs) NAPE(O-18:1/20:4/18:0) and/or NAPE(P-18:0/20:4/18:0) (β: 0.13; 95% CI: 0.11, 0.14), lysophosphatidylinositol (LPI) (22:6/0:0) (β: 0.14; 95% CI: 0.12, 0.17), and fatty acid (FA) (22:6) (β: 0.15; 95% CI: 0.13, 0.17). The "fried snacks, sweets, high-fat dairy" pattern was associated with 12 lipids, including PC(16:0/22:6) (β: -0.08; 95% CI: -0.09, -0.06) and FA (22:6) (β: 0.14; 95% CI: -0.17, -0.10). The "fruits, vegetables, nuts, and legumes" pattern was associated with 5 metabolites including proline betaine (β: 0.17; 95% CI: 0.09, 0.25) (P < 0.0002). CONCLUSIONS Three predominant dietary patterns in US South Asians are associated with circulating metabolites differentiated by lipids including glycerophospholipids and PUFAs and the amino acid proline betaine.
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Affiliation(s)
- Meghana D Gadgil
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Alka M Kanaya
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caroline Sands
- National Phenome Centre, Imperial College London, London, United Kingdom
| | - Elena Chekmeneva
- National Phenome Centre, Imperial College London, London, United Kingdom
| | - Matthew R Lewis
- National Phenome Centre, Imperial College London, London, United Kingdom
| | - Namratha R Kandula
- Division of General Internal Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David M Herrington
- Section on Cardiovascular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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8
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Skov Kragsnaes M, Miguens Blanco J, Chekmeneva E, Salam A, Lewis MR, Kjeldsen J, Horn HC, Munk HL, Pedersen JK, Marchesi J, Ellingsen T. POS1083 INCREASED INTESTINAL PERMEABILITY IN PATIENTS WITH PSORIATIC ARTHRITIS CLASSIFIED AS TREATMENT FAILURES DURING THE 26-WEEK FLORA TRIAL. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundChanges in the integrity of the intestinal wall may be implicated in the gut-joint axis of inflammatory arthritis.1 Yet, the gut barrier is only poorly evaluated in psoriatic arthritis (PsA).2ObjectivesIn this exploratory study, we evaluated intestinal permeability before and 26 weeks after one faecal microbiota transplantation (FMT) or sham intervention in adults with PsA.MethodsWe have previously reported the clinical results of a 26-week, double-blind, parallel-group, 1:1 randomised, sham-controlled, superiority trial of gastroscopic-guided FMT as an add-on treatment to methotrexate in 31 adults with active peripheral PsA (FLORA trial, NCT03058900).3 The primary efficacy endpoint was the proportion of participants who experienced treatment failure through 26 weeks, defined as need for more than one intra-articular glucocorticoid injection and/or anti-TNFα inhibition. We encouraged patients not to take nonsteroidal anti-inflammatory drugs during the trial. The FMT material was obtained from one of four healthy blood donors. As part of the trial, we performed a lactulose and mannitol test (L:M test) at baseline (n=31) and at the final 26-week visit (n=26) to assess the permeability of the intestinal wall (higher L:M ratios indicate higher permeability). After an overnight fasting, patients provided a urine sample before ingesting 10 g of lactulose and 5 g of D-mannitol. Samples were collected after 3 hours and stored at −80°C until analysis. No food or drinking (except for water) was allowed during the test. We measured the lactulose-to-mannitol ratio in the urine samples using a Waters Acquity UPLC system coupled to a high-resolution mass spectrometer Waters Xevo G2 QToF (Waters Corp., Milford, MA, USA). MassLynx software (Waters Corporation) was used for data acquisition and visual inspection. We used StataSE-64 to perform the Wilcoxon rank sum and the matched-pairs signed-rank test. Data is presented as median and range. The level of significance was set to 0.05.ResultsAt baseline, no significant difference was observed in the L:M ratio between donors (n=4) and patients (n=31) (0.0065 [0–0.063] vs 0.014 [0–0.28]; p=0.50). The L:M ratio increased from baseline to week 26 in both the FMT (0.0020 [-0.27 – 0.32] and the sham group (0.0046 [-0.012 – 0.088]), but only in the sham group differed the baseline L:M ratio significantly from the one measured at week 26 (p=0.92 [FMT] and p=0.032 [sham]). The patients who were classified as treatment failures during the trial (n=7) had a significantly higher L:M ratio at week 26 compared to the patients who were non-failures (n=19) (0.027 [0.017 – 0.33]) vs 0.012 [0 – 0.064], p=0.01), please see Figure 1.Figure 1.L:M ratios at week 26 in treatment failures (n=7) and non-failures (n=19), respectively. Higher L:M ratios indicate higher intestinal permeability.ConclusionIn the FLORA trial, intestinal permeability evaluated by the L:M test did not differ significantly between donors and patients at baseline. Whether the higher intestinal permeability observed in patients classified as treatment failures compared to non-failures at week 26 can be attributed to differences in disease activity and/or the instigation of additional immunosuppression in the failure group during the trial needs further investigation.References[1]Gracey E, Vereecke L, McGovern D, et al. Revisiting the gut-joint axis: links between gut inflammation and spondyloarthritis. Nat Rev Rheumatol. 2020;16(8):415-433.[2]Hecquet S, Totoson P, Martin H, et al. Intestinal permeability in spondyloarthritis and rheumatoid arthritis: A systematic review of the literature. Semin Arthritis Rheum. 2021;51(4):712-718.[3]Kragsnaes MS, Kjeldsen J, Horn HC, et al. Safety and efficacy of faecal microbiota transplantation for active peripheral psoriatic arthritis: an exploratory randomised placebo-controlled trial. Ann Rheum Dis. 2021;80(9):1158-1167.Disclosure of InterestsNone declared
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9
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Climaco Pinto R, Karaman I, Lewis MR, Hällqvist J, Kaluarachchi M, Graça G, Chekmeneva E, Durainayagam B, Ghanbari M, Ikram MA, Zetterberg H, Griffin J, Elliott P, Tzoulaki I, Dehghan A, Herrington D, Ebbels T. Finding Correspondence between Metabolomic Features in Untargeted Liquid Chromatography-Mass Spectrometry Metabolomics Datasets. Anal Chem 2022; 94:5493-5503. [PMID: 35360896 PMCID: PMC9008693 DOI: 10.1021/acs.analchem.1c03592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Integration
of multiple datasets can greatly enhance bioanalytical
studies, for example, by increasing power to discover and validate
biomarkers. In liquid chromatography–mass spectrometry (LC–MS)
metabolomics, it is especially hard to combine untargeted datasets
since the majority of metabolomic features are not annotated and thus
cannot be matched by chemical identity. Typically, the information
available for each feature is retention time (RT), mass-to-charge
ratio (m/z), and feature intensity
(FI). Pairs of features from the same metabolite in separate datasets
can exhibit small but significant differences, making matching very
challenging. Current methods to address this issue are too simple
or rely on assumptions that cannot be met in all cases. We present
a method to find feature correspondence between two similar LC–MS
metabolomics experiments or batches using only the features’
RT, m/z, and FI. We demonstrate
the method on both real and synthetic datasets, using six orthogonal
validation strategies to gauge the matching quality. In our main example,
4953 features were uniquely matched, of which 585 (96.8%) of 604 manually
annotated features were correct. In a second example, 2324 features
could be uniquely matched, with 79 (90.8%) out of 87 annotated features
correctly matched. Most of the missed annotated matches are between
features that behave very differently from modeled inter-dataset shifts
of RT, MZ, and FI. In a third example with simulated data with 4755
features per dataset, 99.6% of the matches were correct. Finally,
the results of matching three other dataset pairs using our method
are compared with a published alternative method, metabCombiner, showing
the advantages of our approach. The method can be applied using M2S
(Match 2 Sets), a free, open-source MATLAB toolbox, available at https://github.com/rjdossan/M2S.
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Affiliation(s)
- Rui Climaco Pinto
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W12 0BZ, U.K.,UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K
| | - Ibrahim Karaman
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W12 0BZ, U.K.,UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K
| | - Matthew R Lewis
- MRC-NIHR National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Jenny Hällqvist
- Centre for Translational Omics, Great Ormond Street Hospital, University College London, London WC1N 1EH, U.K.,Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London WC1N 3BG, U.K
| | - Manuja Kaluarachchi
- UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K.,Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Gonçalo Graça
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Elena Chekmeneva
- MRC-NIHR National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Brenan Durainayagam
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W12 0BZ, U.K.,UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, 431 41 Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 413 45 Mölndal, Sweden.,Department of Neurodegenerative Disease, University College London, Queen Square, London WC1N 3BG, U.K.,UK Dementia Research Institute, University College London, London WC1N 3BG, U.K
| | - Julian Griffin
- UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K.,Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W12 0BZ, U.K.,UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W12 0BZ, U.K.,Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, 451 10 Ioannina, Greece
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W12 0BZ, U.K.,UK Dementia Research Institute, Imperial College London, London W12 0BZ, U.K.,Department of Epidemiology, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - David Herrington
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Timothy Ebbels
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, U.K
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10
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Mehta R, Chekmeneva E, Jackson H, Sands C, Mills E, Arancon D, Li HK, Arkell P, Rawson TM, Hammond R, Amran M, Haber A, Cooke GS, Noursadeghi M, Kaforou M, Lewis MR, Takats Z, Sriskandan S. Antiviral metabolite 3'-deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19. Med 2022; 3:204-215.e6. [PMID: 35128501 PMCID: PMC8801973 DOI: 10.1016/j.medj.2022.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/14/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing. METHODS Using untargeted high-resolution liquid chromatography coupled with mass spectrometry, we compared the admission serum metabolome of emergency department patients with viral infections (including COVID-19), bacterial infections, inflammatory conditions, and healthy controls. Sera from an independent cohort of emergency department patients admitted with viral or bacterial infections underwent profiling to validate findings. Associations between whole-blood gene expression and the identified metabolite of interest were examined. FINDINGS 3'-Deoxy-3',4'-didehydro-cytidine (ddhC), a free base of the only known human antiviral small molecule ddhC-triphosphate (ddhCTP), was detected for the first time in serum. When comparing 60 viral with 101 non-viral cases in the discovery cohort, ddhC was the most significantly differentially abundant metabolite, generating an area under the receiver operating characteristic curve (AUC) of 0.954 (95% CI: 0.923-0.986). In the validation cohort, ddhC was again the most significantly differentially abundant metabolite when comparing 40 viral with 40 bacterial cases, generating an AUC of 0.81 (95% CI 0.708-0.915). Transcripts of viperin and CMPK2, enzymes responsible for ddhCTP synthesis, were among the five genes most highly correlated with ddhC abundance. CONCLUSIONS The antiviral precursor molecule ddhC is detectable in serum and an accurate marker for acute viral infection. Interferon-inducible genes viperin and CMPK2 are implicated in ddhC production in vivo. These findings highlight a future diagnostic role for ddhC in viral diagnosis, pandemic preparedness, and acute infection management. FUNDING NIHR Imperial BRC; UKRI.
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Affiliation(s)
- Ravi Mehta
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Elena Chekmeneva
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Heather Jackson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Caroline Sands
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Ewurabena Mills
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | | | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2AZ, UK
| | - Paul Arkell
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Timothy M. Rawson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
- Division of Infection & Immunity, University College London, London WC1 E6BT, UK
| | - Robert Hammond
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Maisarah Amran
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Anna Haber
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Graham S. Cooke
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College London, London WC1 E6BT, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Matthew R. Lewis
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Zoltan Takats
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2AZ, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London W12 0NN, UK
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11
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Albreht A, Hussain H, Jiménez B, Yuen AHY, Whiley L, Witt M, Lewis MR, Chekmeneva E. Structure Elucidation and Mitigation of Endogenous Interferences in LC-MS-Based Metabolic Profiling of Urine. Anal Chem 2022; 94:1760-1768. [PMID: 35026111 DOI: 10.1021/acs.analchem.1c04378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is the main workhorse of metabolomics owing to its high degree of analytical sensitivity and specificity when measuring diverse chemistry in complex biological samples. LC-MS-based metabolic profiling of human urine, a biofluid of primary interest for clinical and biobank studies, is not widely considered to be compromised by the presence of endogenous interferences and is often accomplished using a simple "dilute-and-shoot" approach. Yet, it is our experience that broad obscuring signals are routinely observed in LC-MS metabolic profiles and represent interferences that lack consideration in the relevant metabolomics literature. In this work, we chromatographically isolated the interfering metabolites from human urine and unambiguously identified them via de novo structure elucidation as two separate proline-containing dipeptides: N,N,N-trimethyl-l-alanine-l-proline betaine (l,l-TMAP) and N,N-dimethyl-l-proline-l-proline betaine (l,l-DMPP), the latter reported here for the first time. Offline LC-MS/MS, magnetic resonance mass spectrometry (MRMS), and nuclear magnetic resonance (NMR) spectroscopy were essential components of this workflow for the full chemical and spectroscopic characterization of these metabolites and for establishing the coexistence of cis and trans isomers of both dipeptides in solution. Analysis of these definitive structures highlighted intramolecular ionic interactions as responsible for slow interconversion between these isomeric forms resulting in their unusually broad elution profiles. Proposed mitigation strategies, aimed at increasing the quality of LC-MS-based urine metabolomics data, include modification of column temperature and mobile-phase pH to reduce the chromatographic footprint of these dipeptides, thereby reducing their interfering effect on the underlying metabolic profiles. Alternatively, sample dilution and internal standardization methods may be employed to reduce or account for the observed effects of ionization suppression on the metabolic profile.
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Affiliation(s)
- Alen Albreht
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.,Analytical, Environmental & Forensic Sciences, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, London SE1 9NH, United Kingdom.,Laboratory for Food Chemistry, Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Humma Hussain
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.,Division of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Beatriz Jiménez
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ada H Y Yuen
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, United Kingdom
| | - Luke Whiley
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom
| | - Matthias Witt
- MRMS Solutions, Bruker Daltonics GmbH & Co. KG, MRMS Solutions, 28359 Bremen, Germany
| | - Matthew R Lewis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, United Kingdom
| | - Elena Chekmeneva
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, United Kingdom
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12
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Ferreira MR, Sands CJ, Li JV, Andreyev JN, Chekmeneva E, Gulliford S, Marchesi J, Lewis MR, Dearnaley DP. Impact of Pelvic Radiation Therapy for Prostate Cancer on Global Metabolic Profiles and Microbiota-Driven Gastrointestinal Late Side Effects: A Longitudinal Observational Study. Int J Radiat Oncol Biol Phys 2021; 111:1204-1213. [PMID: 34352290 PMCID: PMC8609156 DOI: 10.1016/j.ijrobp.2021.07.1713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Radiation therapy to the prostate and pelvic lymph nodes (PLNRT) is part of the curative treatment of high-risk prostate cancer. Yet, the broader influence of radiation therapy on patient physiology is poorly understood. We conducted comprehensive global metabolomic profiling of urine, plasma, and stools sampled from patients undergoing PLNRT for high-risk prostate cancer. METHODS AND MATERIALS Samples were taken from 32 patients at 6 timepoints: baseline, 2 to 3 and 4 to 5 weeks of PLNRT; and 3, 6, and 12 months after PLNRT. We characterized the global metabolome of urine and plasma using 1H nuclear magnetic resonance spectroscopy and ultraperformance liquid chromatography-mass spectrometry, and of stools with nuclear magnetic resonance. Linear mixed-effects modeling was used to investigate metabolic changes between timepoints for each biofluid and assay and determine metabolites of interest. RESULTS Metabolites in urine, plasma and stools changed significantly after PLNRT initiation. Metabolic profiles did not return to baseline up to 1 year post-PLNRT in any biofluid. Molecules associated with cardiovascular risk were increased in plasma. Pre-PLNRT fecal butyrate levels directly associated with increasing gastrointestinal side effects, as did a sharper fall in those levels during and up to 1 year postradiation therapy, mirroring our previous results with metataxonomics. CONCLUSIONS We showed for the first time that an overall metabolic effect is observed in patients undergoing PLNRT up to 1 year posttreatment. These metabolic changes may effect on long-term morbidity after treatment, which warrants further investigation.
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Affiliation(s)
- Miguel R Ferreira
- Academic Radiotherapy Department, The Institute of Cancer Research, London, United Kingdom; Clinical Oncology Department, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Clinical Oncology Department, Guys and St Thomas NHS Foundation Trust, London, United Kingdom; School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom.
| | - Caroline J Sands
- National Phenome Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jia V Li
- Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom
| | - Jervoise N Andreyev
- Gastroenterology Department, United Lincolnshire Hospitals NHS Trust, Lincolnshire, United Kingdom
| | - Elena Chekmeneva
- National Phenome Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Sarah Gulliford
- Academic Radiotherapy Department, The Institute of Cancer Research, London, United Kingdom; Radiotherapy Department, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Julian Marchesi
- Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom; School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Matthew R Lewis
- National Phenome Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - David P Dearnaley
- Academic Radiotherapy Department, The Institute of Cancer Research, London, United Kingdom; Clinical Oncology Department, The Royal Marsden NHS Foundation Trust, London, United Kingdom
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13
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Wolfer AM, Correia GDS, Sands CJ, Camuzeaux S, Yuen AHY, Chekmeneva E, Takáts Z, Pearce JTM, Lewis MR. peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets. Bioinformatics 2021; 37:4886-4888. [PMID: 34125879 PMCID: PMC8665750 DOI: 10.1093/bioinformatics/btab433] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/09/2021] [Accepted: 06/12/2021] [Indexed: 11/12/2022] Open
Abstract
Untargeted LC-MS profiling assays are capable of measuring thousands of chemical compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC-MS profiling experiments. It takes advantage of chromatographic and spectral databases and prior information of sample matrix composition to generate annotated and interpretable metabolic phenotypic datasets and power workflows for real time data quality assessment. AVAILABILITY peakPantheR is available via Bioconductor (https://bioconductor.org/packages/peakPantheR/). Documentation and worked examples are available at https://phenomecentre.github.io/peakPantheR.github.io/ and https://github.com/phenomecentre/metabotyping-dementia-urine. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Arnaud M Wolfer
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Gonçalo D S Correia
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Caroline J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Stephane Camuzeaux
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Ada H Y Yuen
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Elena Chekmeneva
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Zoltán Takáts
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
| | - Jake T M Pearce
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK
| | - Matthew R Lewis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London, UK.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, UK
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14
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Wood AC, Saylor G, Tzoulaki I, Greenland P, Tracy RP, Post WS, Lindon J, Wassel CL, Phan M, Momin S, Ebbels T, Boulange C, Graça G, Karaman I, Gadghil M, Chekmeneva E, Kaluarachchi M, Elliott P, Herrington DM. Abstract MP09: Untargeted
1
H Nmr Metabolomics Metabolomic Analysis Reveals Pathways Of Protection Between Mediterranean-style Diet And Incident Cardiovascular Disease In The Multi-ethnic Study Of Atherosclerosis. Circulation 2021. [DOI: 10.1161/circ.143.suppl_1.mp09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
The metabolites associated with a Mediterranean-style (AMED) diet may give insight into why AMED is robustly associated with protection against CVD. Previous investigations seeking to identify these have been limited by the use of modest sample sizes and targeted assays.
Methods:
Using samples from the Multi-Ethnic Study of Atherosclerosis (MESA), we conducted untargeted
1
H NMR spectroscopy (600 MHz) with internal and external annotation on the sera of ~3,698 participants, ages 45-84, who were free from overt CVD. We included data on baseline dietary intake (self-reported), and all incident CVD events (excluding stroke) over a 10-year period. From >100,000 spectral features, 845 significant associations (P<2.2*10
-6
) were identified via linear regression, and reduced to a putative list of 46 via elastic net regularized models. Hierarchical clustering identified 11 feature groups, from which cluster scores were constructed. The ‘mediate’ package in R used bootstrapping (1000 simulations) to partition the association between AMED and incident CVD into the effects of dietary intake on CVD which are mediated by the metabolomic cluster scores (the “indirect” / mediated effects) and those effects which are not (“direct effects”). All association analyses controlled for age, sex, ethnicity, data collection site and daily caloric intake.
Results:
AMED score was associated with reductions in the incidence of CVD (HR=0.95; 95% CI: 0.91 - 0.99; P=0.02). All metabolomic cluster scores were associated with AMED (all P<2*10
-06
;
Table 1
), with 6 significantly associated with incident CVD (all P<2.0*10
-4
) in the expected direction given their associations with AMED score. Four of these six significantly mediated the association of AMED score with incident CVD (P<0.05;
Table 1
).
Conclusions:
These preliminary data suggest that specific molecules, if replicated in other studies, hold promise to identify the underlying pathways by which an AMED diet offers protection against CVD.
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15
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Takis PG, Jiménez B, Al-Saffar NMS, Harvey N, Chekmeneva E, Misra S, Lewis MR. A Computationally Lightweight Algorithm for Deriving Reliable Metabolite Panel Measurements from 1D 1H NMR. Anal Chem 2021; 93:4995-5000. [PMID: 33733737 PMCID: PMC8041249 DOI: 10.1021/acs.analchem.1c00113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/05/2021] [Indexed: 12/23/2022]
Abstract
Small Molecule Enhancement SpectroscopY (SMolESY) was employed to develop a unique and fully automated computational solution for the assignment and integration of 1H nuclear magnetic resonance (NMR) signals from metabolites in challenging matrices containing macromolecules (herein blood products). Sensitive and reliable quantitation is provided by instant signal deconvolution and straightforward integration bolstered by spectral resolution enhancement and macromolecular signal suppression. The approach is highly efficient, requiring only standard one-dimensional 1H NMR spectra and avoiding the need for sample preprocessing, complex deconvolution, and spectral baseline fitting. The performance of the algorithm, developed using >4000 NMR serum and plasma spectra, was evaluated using an additional >8800 spectra, yielding an assignment accuracy greater than 99.5% for all 22 metabolites targeted. Further validation of its quantitation capabilities illustrated a reliable performance among challenging phenotypes. The simplicity and complete automation of the approach support the application of NMR-based metabolite panel measurements in clinical and population screening applications.
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Affiliation(s)
- Panteleimon G. Takis
- National
Phenome Centre, Imperial College London, Hammer-smith Campus, IRDB Building, London W12 0NN, United Kingdom
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Beatriz Jiménez
- National
Phenome Centre, Imperial College London, Hammer-smith Campus, IRDB Building, London W12 0NN, United Kingdom
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Nada M. S. Al-Saffar
- National
Phenome Centre, Imperial College London, Hammer-smith Campus, IRDB Building, London W12 0NN, United Kingdom
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Nikita Harvey
- National
Phenome Centre, Imperial College London, Hammer-smith Campus, IRDB Building, London W12 0NN, United Kingdom
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Elena Chekmeneva
- National
Phenome Centre, Imperial College London, Hammer-smith Campus, IRDB Building, London W12 0NN, United Kingdom
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Shivani Misra
- Section of
Metabolic Medicine, Division of Diabetes, Endocrinology and Metabolism,
Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary’s Campus, London W1 1PG, United Kingdom
| | - Matthew R. Lewis
- National
Phenome Centre, Imperial College London, Hammer-smith Campus, IRDB Building, London W12 0NN, United Kingdom
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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16
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Sands CJ, Gómez-Romero M, Correia G, Chekmeneva E, Camuzeaux S, Izzi-Engbeaya C, Dhillo WS, Takats Z, Lewis MR. Representing the Metabolome with High Fidelity: Range and Response as Quality Control Factors in LC-MS-Based Global Profiling. Anal Chem 2021; 93:1924-1933. [PMID: 33448796 DOI: 10.1021/acs.analchem.0c03848] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is a powerful and widely used technique for measuring the abundance of chemical species in living systems. Its sensitivity, analytical specificity, and direct applicability to biofluids and tissue extracts impart great promise for the discovery and mechanistic characterization of biomarker panels for disease detection, health monitoring, patient stratification, and treatment personalization. Global metabolic profiling applications yield complex data sets consisting of multiple feature measurements for each chemical species observed. While this multiplicity can be useful in deriving enhanced analytical specificity and chemical identities from LC-MS data, data set inflation and quantitative imprecision among related features is problematic for statistical analyses and interpretation. This Perspective provides a critical evaluation of global profiling data fidelity with respect to measurement linearity and the quantitative response variation observed among components of the spectra. These elements of data quality are widely overlooked in untargeted metabolomics yet essential for the generation of data that accurately reflect the metabolome. Advanced feature filtering informed by linear range estimation and analyte response factor assessment is advocated as an attainable means of controlling LC-MS data quality in global profiling studies and exemplified herein at both the feature and data set level.
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Affiliation(s)
- Caroline J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - María Gómez-Romero
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Gonçalo Correia
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Elena Chekmeneva
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Stephane Camuzeaux
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Chioma Izzi-Engbeaya
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0HS, United Kingdom
| | - Waljit S Dhillo
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0HS, United Kingdom
| | - Zoltan Takats
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Matthew R Lewis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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17
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Lau CHE, Taylor-Bateman V, Vorkas PA, Graça G, Vu THT, Hou L, Chekmeneva E, Ebbels TMD, Chan Q, Van Horn L, Holmes E. Metabolic Signatures of Gestational Weight Gain and Postpartum Weight Loss in a Lifestyle Intervention Study of Overweight and Obese Women. Metabolites 2020; 10:metabo10120498. [PMID: 33291639 PMCID: PMC7761920 DOI: 10.3390/metabo10120498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Overweight and obesity amongst women of reproductive age are increasingly common in developed economies and are shown to adversely affect birth outcomes and both childhood and adulthood health risks in the offspring. Metabolic profiling in conditions of overweight and obesity in pregnancy could potentially be applied to elucidate the molecular basis of the adverse effects of gestational weight gain (GWG) and postpartum weight loss (WL) on future risks for cardiovascular disease (CVD) and other chronic diseases. Methods: Biofluid samples were collected from 114 ethnically diverse pregnant women with body mass index (BMI) between 25 and 40 kg/m2 from Chicago (US), as part of a randomized lifestyle intervention trial (Maternal Offspring Metabolics: Family Intervention Trial; NCT01631747). At 15 weeks, 35 weeks of gestation, and at 1 year postpartum, the blood plasma lipidome and metabolic profile of urine samples were analyzed by liquid chromatography mass spectrometry (LC-MS) and 1H nuclear magnetic resonance spectroscopy (1H NMR) respectively. Results: Urinary 4-deoxyerythronic acid and 4-deoxythreonic acid were found to be positively correlated to BMI. Seventeen plasma lipids were found to be associated with GWG and 16 lipids were found to be associated with WL, which included phosphatidylinositols (PI), phosphatidylcholines (PC), lysophospholipids (lyso-), sphingomyelins (SM) and ether phosphatidylcholine (PC-O). Three phospholipids found to be positively associated with GWG all contained palmitate side-chains, and amongst the 14 lipids that were negatively associated with GWG, seven were PC-O. Six of eight lipids found to be negatively associated with WL contained an 18:2 fatty acid side-chain. Conclusions: Maternal obesity was associated with characteristic urine and plasma metabolic phenotypes, and phospholipid profile was found to be associated with both GWG and postpartum WL in metabolically healthy pregnant women with overweight/obesity. Postpartum WL may be linked to the reduction in the intake of linoleic acid/conjugated linoleic acid food sources in our study population.
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Affiliation(s)
- Chung-Ho E. Lau
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK;
- Correspondence: (C.-H.E.L.); (E.H.)
| | - Victoria Taylor-Bateman
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Panagiotis A. Vorkas
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece
| | - Gonçalo Graça
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK; (G.G.); (T.M.D.E.)
| | - Thanh-Huyen T. Vu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (T.-H.T.V.); (L.H.); (L.V.H.)
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (T.-H.T.V.); (L.H.); (L.V.H.)
| | - Elena Chekmeneva
- National Phenome Centre and Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, UK;
| | - Timothy M. D. Ebbels
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK; (G.G.); (T.M.D.E.)
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK;
- MRC Centre for Environment and Health, Imperial College London, London W2 1PG, UK
| | - Linda Van Horn
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (T.-H.T.V.); (L.H.); (L.V.H.)
| | - Elaine Holmes
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (C.-H.E.L.); (E.H.)
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18
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Takis PG, Jiménez B, Sands CJ, Chekmeneva E, Lewis MR. SMolESY: an efficient and quantitative alternative to on-instrument macromolecular 1H-NMR signal suppression. Chem Sci 2020; 11:6000-6011. [PMID: 34094091 PMCID: PMC8159292 DOI: 10.1039/d0sc01421d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 12/23/2022] Open
Abstract
One-dimensional (1D) proton-nuclear magnetic resonance (1H-NMR) spectroscopy is an established technique for measuring small molecules in a wide variety of complex biological sample types. It is demonstrably reproducible, easily automatable and consequently ideal for routine and large-scale application. However, samples containing proteins, lipids, polysaccharides and other macromolecules produce broad signals which overlap and convolute those from small molecules. NMR experiment types designed to suppress macromolecular signals during acquisition may be additionally performed, however these approaches add to the overall sample analysis time and cost, especially for large cohort studies, and fail to produce reliably quantitative data. Here, we propose an alternative way of computationally eliminating macromolecular signals, employing the mathematical differentiation of standard 1H-NMR spectra, producing small molecule-enhanced spectra with preserved quantitative capability and increased resolution. Our approach, presented in its simplest form, was implemented in a cheminformatic toolbox and successfully applied to more than 3000 samples of various biological matrices rich or potentially rich with macromolecules, offering an efficient alternative to on-instrument experimentation, facilitating NMR use in routine and large-scale applications.
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Affiliation(s)
- Panteleimon G Takis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus London SW7 2AZ UK
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus IRDB Building London W12 0NN UK
| | - Beatriz Jiménez
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus London SW7 2AZ UK
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus IRDB Building London W12 0NN UK
| | - Caroline J Sands
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus London SW7 2AZ UK
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus IRDB Building London W12 0NN UK
| | - Elena Chekmeneva
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus London SW7 2AZ UK
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus IRDB Building London W12 0NN UK
| | - Matthew R Lewis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus London SW7 2AZ UK
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus IRDB Building London W12 0NN UK
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19
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Gibson R, Lau CHE, Loo RL, Ebbels TMD, Chekmeneva E, Dyer AR, Miura K, Ueshima H, Zhao L, Daviglus ML, Stamler J, Van Horn L, Elliott P, Holmes E, Chan Q. The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP). Am J Clin Nutr 2020; 111:280-290. [PMID: 31782492 PMCID: PMC6997096 DOI: 10.1093/ajcn/nqz293] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/30/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Results from observational studies regarding associations between fish (including shellfish) intake and cardiovascular disease risk factors, including blood pressure (BP) and BMI, are inconsistent. OBJECTIVE To investigate associations of fish consumption and associated urinary metabolites with BP and BMI in free-living populations. METHODS We used cross-sectional data from the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP), including 4680 men and women (40-59 y) from Japan, China, the United Kingdom, and United States. Dietary intakes were assessed by four 24-h dietary recalls and BP from 8 measurements. Urinary metabolites (2 timed 24-h urinary samples) associated with fish intake acquired from NMR spectroscopy were identified. Linear models were used to estimate BP and BMI differences across categories of intake and per 2 SD higher intake of fish and its biomarkers. RESULTS No significant associations were observed between fish intake and BP. There was a direct association with fish intake and BMI in the Japanese population sample (P trend = 0.03; fully adjusted model). In Japan, trimethylamine-N-oxide (TMAO) and taurine, respectively, demonstrated area under the receiver operating characteristic curve (AUC) values of 0.81 and 0.78 in discriminating high against low fish intake, whereas homarine (a metabolite found in shellfish muscle) demonstrated an AUC of 0.80 for high/nonshellfish intake. Direct associations were observed between urinary TMAO and BMI for all regions except Japan (P < 0.0001) and in Western populations between TMAO and BP (diastolic blood pressure: mean difference 1.28; 95% CI: 0.55, 2.02 mmHg; P = 0.0006, systolic blood pressure: mean difference 1.67; 95% CI: 0.60, 2.73 mmHg; P = 0.002). CONCLUSIONS Urinary TMAO showed a stronger association with fish intake in the Japanese compared with the Western population sample. Urinary TMAO was directly associated with BP in the Western but not the Japanese population sample. Associations between fish intake and its biomarkers and downstream associations with BP/BMI appear to be context specific. INTERMAP is registered at www.clinicaltrials.gov as NCT00005271.
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Affiliation(s)
- Rachel Gibson
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Nutritional Sciences, School of Life Course Sciences, King's College London, London, United Kingdom
| | - Chung-Ho E Lau
- Division of Diabetes Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Ruey Leng Loo
- Institute of Health Futures, Murdoch University, Perth, Western Australia, Australia
| | - Timothy M D Ebbels
- Division of System Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Elena Chekmeneva
- National Institute for Health Research–British Research Council, Clinical Phenotyping Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Alan R Dyer
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Katsuyuki Miura
- Department of Public Health, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Hirotsugu Ueshima
- Department of Public Health, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Liancheng Zhao
- Department of Epidemiology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Linda Van Horn
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Health Data Research UK London, Imperial College London, London, United Kingdom
| | - Elaine Holmes
- Division of Diabetes Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Institute of Health Futures, Murdoch University, Perth, Western Australia, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
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20
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Tzoulaki I, Castagné R, Boulangé CL, Karaman I, Chekmeneva E, Evangelou E, Ebbels TMD, Kaluarachchi MR, Chadeau-Hyam M, Mosen D, Dehghan A, Moayyeri A, Ferreira DLS, Guo X, Rotter JI, Taylor KD, Kavousi M, de Vries PS, Lehne B, Loh M, Hofman A, Nicholson JK, Chambers J, Gieger C, Holmes E, Tracy R, Kooner J, Greenland P, Franco OH, Herrington D, Lindon JC, Elliott P. Serum metabolic signatures of coronary and carotid atherosclerosis and subsequent cardiovascular disease. Eur Heart J 2019; 40:2883-2896. [PMID: 31102408 PMCID: PMC7963131 DOI: 10.1093/eurheartj/ehz235] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/21/2018] [Accepted: 05/13/2019] [Indexed: 12/31/2022] Open
Abstract
AIMS To characterize serum metabolic signatures associated with atherosclerosis in the coronary or carotid arteries and subsequently their association with incident cardiovascular disease (CVD). METHODS AND RESULTS We used untargeted one-dimensional (1D) serum metabolic profiling by proton nuclear magnetic resonance spectroscopy (1H NMR) among 3867 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), with replication among 3569 participants from the Rotterdam and LOLIPOP studies. Atherosclerosis was assessed by coronary artery calcium (CAC) and carotid intima-media thickness (IMT). We used multivariable linear regression to evaluate associations between NMR features and atherosclerosis accounting for multiplicity of comparisons. We then examined associations between metabolites associated with atherosclerosis and incident CVD available in MESA and Rotterdam and explored molecular networks through bioinformatics analyses. Overall, 30 1H NMR measured metabolites were associated with CAC and/or IMT, P = 1.3 × 10-14 to 1.0 × 10-6 (discovery) and P = 5.6 × 10-10 to 1.1 × 10-2 (replication). These associations were substantially attenuated after adjustment for conventional cardiovascular risk factors. Metabolites associated with atherosclerosis revealed disturbances in lipid and carbohydrate metabolism, branched chain, and aromatic amino acid metabolism, as well as oxidative stress and inflammatory pathways. Analyses of incident CVD events showed inverse associations with creatine, creatinine, and phenylalanine, and direct associations with mannose, acetaminophen-glucuronide, and lactate as well as apolipoprotein B (P < 0.05). CONCLUSION Metabolites associated with atherosclerosis were largely consistent between the two vascular beds (coronary and carotid arteries) and predominantly tag pathways that overlap with the known cardiovascular risk factors. We present an integrated systems network that highlights a series of inter-connected pathways underlying atherosclerosis.
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Affiliation(s)
- Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, University Campus Road 455 00, Ioannina, Greece
- Dementia Research Institute, Imperial College London, Norfolk Place, London, UK
| | - Raphaële Castagné
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- LEASP, UMR 1027, Inserm-Université Toulousse III Paul Sabatier, Toulousse, France
| | - Claire L Boulangé
- Metabometrix Ltd, Imperial Incubator, Bessemer Building, Prince Consort Road, London, UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Ibrahim Karaman
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
- Dementia Research Institute, Imperial College London, Norfolk Place, London, UK
| | - Elena Chekmeneva
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, University Campus Road 455 00, Ioannina, Greece
| | - Timothy M D Ebbels
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Manuja R Kaluarachchi
- Metabometrix Ltd, Imperial Incubator, Bessemer Building, Prince Consort Road, London, UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
| | - David Mosen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
- Dementia Research Institute, Imperial College London, Norfolk Place, London, UK
| | - Alireza Moayyeri
- Farr Institute of Health Informatics Research, University College London Institute of Health Informatics, 222 Euston Road, London, UK
| | - Diana L Santos Ferreira
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfiled Grove, Bristol, UK
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
- Department of Medicine, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
- Department of Medicine, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
- Department of Medicine, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, University Medical Center Rotterdam, CA Rotterdam, the Netherlands
| | - Paul S de Vries
- Department of Epidemiology, Erasmus University Medical Center, University Medical Center Rotterdam, CA Rotterdam, the Netherlands
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX, USA
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, University Medical Center Rotterdam, CA Rotterdam, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Jeremy K Nicholson
- Metabometrix Ltd, Imperial Incubator, Bessemer Building, Prince Consort Road, London, UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - John Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Rd, Harrow, UK
| | - Christian Gieger
- German Research Centre for Environmental Health, Helmholtz Zentrum München, Ingolstädter Landstraße 1, D Neuherberg, Germany
| | - Elaine Holmes
- Metabometrix Ltd, Imperial Incubator, Bessemer Building, Prince Consort Road, London, UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Russell Tracy
- M.D. College of Medicine University of Vermont, The Robert Larner, Given Medical Bldg, E-126, 89 Beaumont Ave, Burlington, VT, USA
| | - Jaspal Kooner
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
- National Heart & Lung Institute, Faculty of Medicine, Imperial College London, Guy Scadding Building, Dovehouse St, Chelsea, London, UK
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, 680 North Lake Shore Drive, Suite, 1400, Chicago, IL, USA
| | - Oscar H Franco
- Department of Medicine, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 W Carson St, Torrance, CA, USA
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, Bern, Switzerland
| | - David Herrington
- Section on Cardiovascular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - John C Lindon
- Metabometrix Ltd, Imperial Incubator, Bessemer Building, Prince Consort Road, London, UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK
- Dementia Research Institute, Imperial College London, Norfolk Place, London, UK
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21
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McGill D, Chekmeneva E, Lindon JC, Takats Z, Nicholson JK. Application of novel solid phase extraction-NMR protocols for metabolic profiling of human urine. Faraday Discuss 2019; 218:395-416. [PMID: 31116193 DOI: 10.1039/c8fd00220g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolite identification and annotation procedures are necessary for the discovery of biomarkers indicative of phenotypes or disease states, but these processes can be bottlenecked by the sheer complexity of biofluids containing thousands of different compounds. Here we describe low-cost novel SPE-NMR protocols utilising different cartridges and conditions, on both natural and artificial urine mixtures, which produce unique retention profiles useful for metabolic profiling. We find that different SPE methods applied to biofluids such as urine can be used to selectively retain metabolites based on compound taxonomy or other key functional groups, reducing peak overlap through concentration and fractionation of unknowns and hence promising greater control over the metabolite annotation/identification process.
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Affiliation(s)
- Daniel McGill
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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22
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Whiley L, Chekmeneva E, Berry DJ, Jiménez B, Yuen AHY, Salam A, Hussain H, Witt M, Takats Z, Nicholson J, Lewis MR. Systematic Isolation and Structure Elucidation of Urinary Metabolites Optimized for the Analytical-Scale Molecular Profiling Laboratory. Anal Chem 2019; 91:8873-8882. [PMID: 31188566 PMCID: PMC6666900 DOI: 10.1021/acs.analchem.9b00241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Annotation
and identification of metabolite biomarkers is critical
for their biological interpretation in metabolic phenotyping studies,
presenting a significant bottleneck in the successful implementation
of untargeted metabolomics. Here, a systematic multistep protocol
was developed for the purification and de novo structural elucidation
of urinary metabolites. The protocol is most suited for instances
where structure elucidation and metabolite annotation are critical
for the downstream biological interpretation of metabolic phenotyping
studies. First, a bulk urine pool was desalted using ion-exchange
resins enabling large-scale fractionation using precise iterations
of analytical scale chromatography. Primary urine fractions were collected
and assembled into a “fraction bank” suitable for long-term
laboratory storage. Secondary and tertiary fractionations exploited
differences in selectivity across a range of reversed-phase chemistries,
achieving the purification of metabolites of interest yielding an
amount of material suitable for chemical characterization. To exemplify
the application of the systematic workflow in a diverse set of cases,
four metabolites with a range of physicochemical properties were selected
and purified from urine and subjected to chemical formula and structure
elucidation by respective magnetic resonance mass spectrometry (MRMS)
and NMR analyses. Their structures were fully assigned as tetrahydropentoxyline,
indole-3-acetic-acid-O-glucuronide, p-cresol glucuronide, and pregnanediol-3-glucuronide. Unused effluent
was collected, dried, and returned to the fraction bank, demonstrating
the viability of the system for repeat use in metabolite annotation
with a high degree of efficiency.
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Affiliation(s)
- Luke Whiley
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom.,UK Dementia Research Institute , Imperial College London, Hammersmith Hospital , Burlington Danes Building , London , W12 0NN , United Kingdom
| | - Elena Chekmeneva
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - David J Berry
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Beatriz Jiménez
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Ada H Y Yuen
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Ash Salam
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Humma Hussain
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Matthias Witt
- Bruker Daltonik GmbH , MRMS Solutions , 28359 Bremen , Germany
| | - Zoltan Takats
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Jeremy Nicholson
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
| | - Matthew R Lewis
- The MRC-NIHR National Phenome Centre and Imperial BRC Clinical Phenotyping Centre , Imperial College London , London , W12 0NN , United Kingdom
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23
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Chekmeneva E, Dos Santos Correia G, Gómez-Romero M, Stamler J, Chan Q, Elliott P, Nicholson JK, Holmes E. Ultra-Performance Liquid Chromatography-High-Resolution Mass Spectrometry and Direct Infusion-High-Resolution Mass Spectrometry for Combined Exploratory and Targeted Metabolic Profiling of Human Urine. J Proteome Res 2018; 17:3492-3502. [PMID: 30183320 PMCID: PMC6184476 DOI: 10.1021/acs.jproteome.8b00413] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The
application of metabolic phenotyping to epidemiological studies
involving thousands of biofluid samples presents a challenge for the
selection of analytical platforms that meet the requirements of high-throughput
precision analysis and cost-effectiveness. Here direct infusion–nanoelectrospray
(DI–nESI) was compared with an ultra-performance liquid chromatography
(UPLC)–high-resolution mass spectrometry (HRMS) method for
metabolic profiling of an exemplary set of 132 human urine samples
from a large epidemiological cohort. Both methods were developed and
optimized to allow the simultaneous collection of high-resolution
urinary metabolic profiles and quantitative data for a selected panel
of 35 metabolites. The total run time for measuring the sample set
in both polarities by UPLC–HRMS was 5 days compared with 9
h by DI–nESI–HRMS. To compare the classification ability
of the two MS methods, we performed exploratory analysis of the full-scan
HRMS profiles to detect sex-related differences in biochemical composition.
Although metabolite identification is less specific in DI–nESI–HRMS,
the significant features responsible for discrimination between sexes
were mostly the same in both MS-based platforms. Using the quantitative
data, we showed that 10 metabolites have strong correlation (Pearson’s r > 0.9 and Passing–Bablok regression slope of 0.8–1.3)
and good agreement assessed by Bland–Altman plots between UPLC–HRMS
and DI–nESI–HRMS and thus can be measured using a cheaper
and less sample- and time-consuming method. A further twenty
metabolites showed acceptable correlation between the two methods
with only five metabolites showing weak correlation (Pearson’s r < 0.4) and poor agreement due to the overestimation
of the results by DI–nESI–HRMS.
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Affiliation(s)
- Elena Chekmeneva
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Gonçalo Dos Santos Correia
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - María Gómez-Romero
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine , Northwestern University , Chicago , Illinois 60611 , United States
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom.,MRC-PHE Centre for Environment and Health, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom.,MRC-PHE Centre for Environment and Health, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom
| | - Jeremy K Nicholson
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Elaine Holmes
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,MRC-PHE Centre for Environment and Health, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom
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24
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Chekmeneva E, Dos Santos Correia G, Chan Q, Wijeyesekera A, Tin A, Young JH, Elliott P, Nicholson JK, Holmes E. Optimization and Application of Direct Infusion Nanoelectrospray HRMS Method for Large-Scale Urinary Metabolic Phenotyping in Molecular Epidemiology. J Proteome Res 2017; 16:1646-1658. [PMID: 28245357 PMCID: PMC5387673 DOI: 10.1021/acs.jproteome.6b01003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Large-scale metabolic profiling requires
the development of novel
economical high-throughput analytical methods to facilitate characterization
of systemic metabolic variation in population phenotypes. We report
a fit-for-purpose direct infusion nanoelectrospray high-resolution
mass spectrometry (DI-nESI-HRMS) method with time-of-flight detection
for rapid targeted parallel analysis of over 40 urinary metabolites.
The newly developed 2 min infusion method requires <10 μL
of urine sample and generates high-resolution MS profiles in both
positive and negative polarities, enabling further data mining and
relative quantification of hundreds of metabolites. Here we present
optimization of the DI-nESI-HRMS method in a detailed step-by-step
guide and provide a workflow with rigorous quality assessment for
large-scale studies. We demonstrate for the first time the application
of the method for urinary metabolic profiling in human epidemiological
investigations. Implementation of the presented DI-nESI-HRMS method
enabled cost-efficient analysis of >10 000 24 h urine samples
from the INTERMAP study in 12 weeks and >2200 spot urine samples
from
the ARIC study in <3 weeks with the required sensitivity and accuracy.
We illustrate the application of the technique by characterizing the
differences in metabolic phenotypes of the USA and Japanese population
from the INTERMAP study.
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Affiliation(s)
- Elena Chekmeneva
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Gonçalo Dos Santos Correia
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London , London W2 1PG, United Kingdom.,MRC-PHE Centre for Environment and Health, Imperial College London , London W2 1PG, United Kingdom
| | - Anisha Wijeyesekera
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom
| | - Adrienne Tin
- Department of Medicine, Johns Hopkins University, School of Medicine , Baltimore, Maryland 21287, United States
| | - Jeffery Hunter Young
- Department of Medicine, Johns Hopkins University, School of Medicine , Baltimore, Maryland 21287, United States
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London , London W2 1PG, United Kingdom.,MRC-PHE Centre for Environment and Health, Imperial College London , London W2 1PG, United Kingdom.,MRC-NIHR National Phenome Centre , London SW7 2AZ, United Kingdom
| | - Jeremy K Nicholson
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.,MRC-NIHR National Phenome Centre , London SW7 2AZ, United Kingdom
| | - Elaine Holmes
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.,MRC-NIHR National Phenome Centre , London SW7 2AZ, United Kingdom
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25
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Gray N, Adesina-Georgiadis K, Chekmeneva E, Plumb RS, Wilson ID, Nicholson JK. Development of a Rapid Microbore Metabolic Profiling Ultraperformance Liquid Chromatography-Mass Spectrometry Approach for High-Throughput Phenotyping Studies. Anal Chem 2016; 88:5742-51. [PMID: 27116471 DOI: 10.1021/acs.analchem.6b00038] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A rapid gradient microbore ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) method has been developed to provide a high-throughput analytical platform for the metabolic phenotyping of urine from large sample cohorts. The rapid microbore metabolic profiling (RAMMP) approach was based on scaling a conventional reversed-phase UPLC-MS method for urinary profiling from 2.1 mm × 100 mm columns to 1 mm × 50 mm columns, increasing the linear velocity of the solvent, and decreasing the gradient time to provide an analysis time of 2.5 min/sample. Comparison showed that conventional UPLC-MS and rapid gradient approaches provided peak capacities of 150 and 50, respectively, with the conventional method detecting approximately 19 000 features compared to the ∼6 000 found using the rapid gradient method. Similar levels of repeatability were seen for both methods. Despite the reduced peak capacity and the reduction in ions detected, the RAMMP method was able to achieve similar levels of group discrimination as conventional UPLC-MS when applied to rat urine samples obtained from investigative studies on the effects of acute 2-bromophenol and chronic acetaminophen administration. When compared to a direct infusion MS method of similar analysis time the RAMMP method provided superior selectivity. The RAMMP approach provides a robust and sensitive method that is well suited to high-throughput metabonomic analysis of complex mixtures such as urine combined with a 5-fold reduction in analysis time compared with the conventional UPLC-MS method.
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Affiliation(s)
- Nicola Gray
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Kyrillos Adesina-Georgiadis
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Elena Chekmeneva
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Robert S Plumb
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Jeremy K Nicholson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom.,MRC-NIHR National Phenome Centre, Division of Computational and Systems Medicine, Department of Surgery and Cancer, IRDB Building, Imperial College London, Hammersmith Hospital , London, W12 0NN, United Kingdom
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26
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Adams H, Chekmeneva E, Hunter CA, Misuraca MC, Navarro C, Turega SM. Correction to “Quantification of the Effect of Conformational Restriction on Supramolecular Effective Molarities”. J Am Chem Soc 2013. [DOI: 10.1021/ja404462f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Adams H, Chekmeneva E, Hunter CA, Misuraca MC, Navarro C, Turega SM. Quantification of the effect of conformational restriction on supramolecular effective molarities. J Am Chem Soc 2013; 135:1853-63. [PMID: 23360075 DOI: 10.1021/ja310221t] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The association constants for a family of 96 closely related zinc porphyrin-pyridine ligand complexes have been measured in two different solvents, toluene and 1,1,2,2-tetrachloroethane (TCE). The zinc porphyrin receptors are equipped with phenol side arms, which can form intramolecular H-bonds with ester or amide side arms on the pyridine ligands. These association constants were used to construct 64 chemical double mutant cycles, which measure the free energy contributions of intramolecular H-bonding interactions to the overall stability of the complexes. Measurement of association constants for the corresponding intermolecular H-bonding interactions allowed determination of the effective molarities (EM) for the intramolecular interactions. Comparison of ligands that feature amide H-bond acceptors and ester H-bonds at identical sites on the ligand framework show that the values of EM are practically identical. Similarly, the values of EM are practically identical in toluene and in TCE. However, comparison of two ligand series that differ by one degree of torsional freedom shows that the values of EM for the flexible ligands are an order of magnitude lower than for the corresponding rigid ligands. This observation holds for a range of different supramolecular architectures with different degrees of receptor-ligand complementarity and suggests that in general the cost of freezing a rotor in supramolecular complexes is of the order of 5 kJ/mol.
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Affiliation(s)
- Harry Adams
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
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28
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Walker MG, Gonzalez V, Chekmeneva E, Thomas JA. Temperature-Switched Binding of a RuII(dppz)/DNA Light-Switch Complex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Walker MG, Gonzalez V, Chekmeneva E, Thomas JA. Temperature-switched binding of a RuII (dppz)/DNA light-switch complex. Angew Chem Int Ed Engl 2012; 51:12107-10. [PMID: 23081806 DOI: 10.1002/anie.201206260] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Michael G Walker
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
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30
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Cavanillas S, Chekmeneva E, Ariño C, Díaz-Cruz JM, Esteban M. Electroanalytical and isothermal calorimetric study of As(III) complexation by the metal poisoning remediators, 2,3-dimercapto-1-propanesulfonate and meso-2,3-dimercaptosuccinic acid. Anal Chim Acta 2012; 746:47-52. [PMID: 22975179 DOI: 10.1016/j.aca.2012.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 07/20/2012] [Accepted: 08/03/2012] [Indexed: 10/28/2022]
Abstract
A recently developed methodology, which combines voltammetry, ITC, ESI-MS and several chemometric tools, has been applied for the first time to the study of As(III) complexes. The ligands considered, DMSA and DMPS, are commonly used to treat heavy metal poisoning. The study yields a reliable and consistent picture of the binding of As(III) by the chelating therapy agents DMSA and DMPS providing an unambiguous description of the stoichiometries of the complexes (ML(2), with the occasional appearance of ML in the case of DMSA), both ligands have stability constants of the same order, with a logβ(2) of 9.2 and 9.8, respectively. These values confirm the potential efficiency of both ligands in the treatment of As(III) poisoning.
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Affiliation(s)
- Santiago Cavanillas
- Departament de Química Analítica, Universitat de Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
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31
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Chekmeneva E, Hunter CA, Misuraca MC, Turega SM. Steric desolvation enhances the effective molarities of intramolecular H-bonding interactions. Org Biomol Chem 2012; 10:6022-31. [DOI: 10.1039/c2ob25372k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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32
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Gilsanz C, Gusmão R, Chekmeneva E, Serrano N, Díaz-Cruz JM, Ariño C, Esteban M. Electroanalysis of the binding and adsorption of Hg2+ with seleno aminoacids by differential pulse and elimination voltammetry at the Au-disk electrode. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.04.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Chekmeneva E, Gusmão R, Díaz-Cruz JM, Ariño C, Esteban M. From cysteine to longer chain thiols: thermodynamic analysis of cadmium binding by phytochelatins and their fragments. Metallomics 2011; 3:838-46. [DOI: 10.1039/c1mt00028d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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34
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Chekmeneva E, DÃaz-Cruz J, Ariño C, Esteban M. Complexation of Hg2+with α-Lipoic and Dihydrolipoic Acids: Study by Differential Pulse Voltammetry on Rotating Au-Disk Electrode and ESI-MS. ELECTROANAL 2010. [DOI: 10.1002/elan.200900299] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Díaz Cruz JM, Sanchís J, Chekmeneva E, Ariño C, Esteban M. Non-linear multivariate curve resolution analysis of voltammetric pH titrations. Analyst 2010; 135:1653-62. [DOI: 10.1039/c0an00088d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chekmeneva E, Díaz-Cruz JM, Ariño C, Esteban M. Study of the Hg2+ binding with chelation therapy agents by differential pulse voltammetry on rotating Au-disk electrode and electrospray ionization mass-spectrometry. Anal Chim Acta 2009; 653:77-85. [DOI: 10.1016/j.aca.2009.08.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/14/2009] [Accepted: 08/28/2009] [Indexed: 10/20/2022]
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Chekmeneva E, Díaz-Cruz JM, Arino C, Esteban M. Binding of Hg2+ with phytochelatins: study by differential pulse voltammetry on rotating Au-disk electrode, electrospray ionization mass-spectrometry, and isothermal titration calorimetry. Environ Sci Technol 2009; 43:7010-7015. [PMID: 19806735 DOI: 10.1021/es901325f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The binding of Hg2+ with synthetic phytochelatins ((gamma-Glu-Cys)n-Gly, PCn, n = 2, 3, 4) was investigated by a recently proposed electroanalytical method, using differential pulse voltammetry on the rotating Au-disk electrode, Electrospray ionization mass-spectrometry (ESI-MS) and isothermaltitration calorimetry (ITC). ESI-MS experiments provided the exact stoichiometries of the complexes formed at different PCn/Hg2+ ratios. Voltammetry provided more detailed information on the complexation processes through the use of multivariate curve resolution by alternating least squares of the data matrix obtained from titrations withfine increments of metal or ligand. The system Hg2+-GSH-PC2 was investigated by voltammetry in order to obtain an estimation of the Hg2+ behavior in the presence of two related ligands. The additional assessment of the stability of Hg2+-PCn complexes was achieved through ITC by using the therapeutic chelator sodium 2,3-dimercaptopropanesulfate (DMPS) over Hg2+-PCn systems. The stability of various Hg2+-PCn complexes and the ability of DMPS to replace PCn from these complexes were examined.
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Affiliation(s)
- Elena Chekmeneva
- Department of Analytical Chemistry, Faculty of Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028, Barcelona, Spain
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Chekmeneva E, Díaz-Cruz JM, Ariño C, Esteban M. A novel differential pulse voltammetric method on rotating Au-disk electrode for the study of Hg2+ binding. J Electroanal Chem (Lausanne) 2009. [DOI: 10.1016/j.jelechem.2009.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Chekmeneva E, Hunter CA, Packer MJ, Turega SM. Evidence for Partially Bound States in Cooperative Molecular Recognition Interfaces [ J. Am. Chem. Soc., 2008, 130, 17718−17725]. J Am Chem Soc 2009. [DOI: 10.1021/ja900730z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chekmeneva E, Hunter CA, Packer MJ, Turega SM. Evidence for partially bound states in cooperative molecular recognition interfaces. J Am Chem Soc 2009; 130:17718-25. [PMID: 19063608 DOI: 10.1021/ja803434z] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A zinc porphyrin equipped with four amide H-bonding sites provides a rigid molecular receptor for the study of cooperative multipoint binding interactions. The interaction of this receptor with a variety of pyridine ligands bearing zero, one, and two H-bonding sites has been studied using UV/vis absorption, (1)H and (31)P NMR spectroscopy, and isothermal titration calorimetry in five different solvents. The results are analyzed in terms of a bound state that populates an ensemble of different complexes in which zero, one, or two of the potential H-bond interactions are formed. The key parameter that determines the behavior of the system is the product of the association constant for the H-bond interaction, K(H), and the effective molarity for the intramolecular interaction, EM. In the system reported here, EM is 0.1-1 M for all of the intramolecular interactions. For strong H-bonds (large K(H) in nonpolar solvents), all of the interactions are formed in the complex and the fully bound state dominates. In this case, additional binding interactions produce incremental increases in complex stability. However, for weaker H-bonds (small K(H) in polar solvents), the formation of additional interactions does not lead to an increase in the overall stability of the complex, due to the population of partially bound states.
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Affiliation(s)
- Elena Chekmeneva
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, and AstraZeneca, Alderley Park, Cheshire SK10 4TG, United Kingdom
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Chekmeneva E, Prohens R, Díaz-Cruz JM, Ariño C, Esteban M. Competitive binding of Cd and Zn with the phytochelatin (gamma-Glu-Cys)4-Gly: comparative study by mass spectrometry, voltammetry-multivariate curve resolution, and isothermal titration calorimetry. Environ Sci Technol 2008; 42:2860-2866. [PMID: 18497135 DOI: 10.1021/es702725a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The competitive binding of Cd2+ and Zn2+ by the phytochelatin (gamma-Glu-Cys)4-Gly (PC4) has been examined using several techniques. Electrospray ionization mass spectrometry is used to determine the stoichiometries of the complexes, while voltammetric data analyzed by multivariate curve resolution with alternating least squares allows one to not only trace the displacement induced by Cd2+ or Zn2+ in the binding of Zn2+ or Cd2+, respectively, by PC4, but also to obtain a complete overview of the processes involved. Isothermal titration calorimetry is used to determine the related binding and thermodynamic parameters. Results obtained via these different techniques are compared and discussed below. The formation of ternary CdZn(PC4) and Cd2Zn(PC4) complexes was observed.
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Affiliation(s)
- Elena Chekmeneva
- Departament de Química Analítica, Facultat de Química and Unitat de Química Fina, Serveis Científico. Tècnics, Universitat de Barcelona Martí i Franquès, 1-11, E - 08028 Barcelona, Spain
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Chekmeneva E, Prohens R, Díaz-Cruz JM, Ariño C, Esteban M. Thermodynamics of Cd2+ and Zn2+ binding by the phytochelatin (γ-Glu-Cys)4-Gly and its precursor glutathione. Anal Biochem 2008; 375:82-9. [DOI: 10.1016/j.ab.2008.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 12/18/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022]
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Sheremet A, Averyaskina E, Chekmeneva E, Ermakov S. Standardless Electrochemical Method for Mercury, Cadmium, Lead and Copper Determination in Aqueous Solution. ELECTROANAL 2007. [DOI: 10.1002/elan.200703971] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chekmeneva E, Díaz-Cruz J, Ariño C, Esteban M. Binding of Cd2+ and Zn2+ with the Phytochelatin (γ-Glu-Cys)4-Gly: A Voltammetric Study Assisted by Multivariate Curve Resolution and Electrospray Ionization Mass Spectrometry. ELECTROANAL 2007. [DOI: 10.1002/elan.200603733] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Chekmeneva E, Díaz-Cruz JM, Ariño C, Esteban M. Identification of heavy metal complexes of a hexapeptide inhibitor of the human immunodeficiency virus integrase protein by using a voltammetric approach. Anal Biochem 2006; 348:252-8. [PMID: 16316619 DOI: 10.1016/j.ab.2005.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 09/27/2005] [Accepted: 10/17/2005] [Indexed: 11/19/2022]
Abstract
Complexation of the hexapeptide Hys-Cys-Lys-Phe-Trp-Trp, inhibitor of the human immunodeficiency virus integrase protein, with the heavy metal ions Cd2+, Pb2+, and Zn2+ has been investigated using differential pulse polarography. In the case of Pb2+, no significant complexation is detected, whereas in the cases of Cd2+ and Zn2+, strong and electrochemically inert ML2 complexes predominate. In contrast, ML complexes are present in a low proportion or are absent. When possible, the corresponding conditional stability constants have been determined at both pH 7.0 and pH 7.5, showing that Zn2+ complexes are slightly more stable than Cd2+ complexes.
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Affiliation(s)
- Elena Chekmeneva
- Departament de Química Analítica, Facultat de Química, Universitat de Barcelona, E-08028 Barcelona, Spain
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