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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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Takis PG, Aggelidou VA, Sands CJ, Louka A. Mapping of 1 H NMR chemical shifts relationship with chemical similarities for the acceleration of metabolic profiling: Application on blood products. Magn Reson Chem 2023; 61:759-769. [PMID: 37666776 PMCID: PMC10946494 DOI: 10.1002/mrc.5392] [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] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
One-dimensional (1D) proton-nuclear magnetic resonance (1 H-NMR) spectroscopy is an established technique for the deconvolution of complex biological sample types via the identification/quantification of small molecules. It is highly reproducible and could be easily automated for small to large-scale bioanalytical, epidemiological, and in general metabolomics studies. However, chemical shift variability is a serious issue that must still be solved in order to fully automate metabolite identification. Herein, we demonstrate a strategy to increase the confidence in assignments and effectively predict the chemical shifts of various NMR signals based upon the simplest form of statistical models (i.e., linear regression). To build these models, we were guided by chemical homology in serum/plasma metabolites classes (i.e., amino acids and carboxylic acids) and similarity between chemical groups such as methyl protons. Our models, built on 940 serum samples and validated in an independent cohort of 1,052 plasma-EDTA spectra, were able to successfully predict the 1 H NMR chemical shifts of 15 metabolites within ~1.5 linewidths (Δv1/2 ) error range on average. This pilot study demonstrates the potential of developing an algorithm for the accurate assignment of 1 H NMR chemical shifts based solely on chemically defined constraints.
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Affiliation(s)
- Panteleimon G. Takis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome Centre, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Varvara A. Aggelidou
- Department of Biological Applications and TechnologiesUniversity of IoanninaIoanninaGreece
| | - Caroline J. Sands
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome Centre, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Alexandra Louka
- Department of Clinical and Experimental Epilepsy, Queen Square Institute of NeurologyUniversity College LondonLondonUK
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3
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Stebbing J, Takis PG, Sands CJ, Maslen L, Lewis MR, Gleason K, Page K, Guttery D, Fernandez-Garcia D, Primrose L, Shaw JA. Comparison of phenomics and cfDNA in a large breast screening population: the Breast Screening and Monitoring Study (BSMS). Oncogene 2023; 42:825-832. [PMID: 36693953 PMCID: PMC10005936 DOI: 10.1038/s41388-023-02591-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/02/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
To assess their roles in breast cancer diagnostics, we aimed to compare plasma cell-free DNA (cfDNA) levels with the circulating metabolome in a large breast screening cohort of women recalled for mammography, including healthy women and women with mammographically detected breast diseases, ductal carcinoma in situ and invasive breast cancer: the Breast Screening and Monitoring Study (BSMS). In 999 women, plasma was analyzed by nuclear magnetic resonance (NMR) and Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and then processed to isolate and quantify total cfDNA. NMR and UPLC-MS results were compared with data for 186 healthy women derived from the AIRWAVE cohort. Results showed no significant differences between groups for all metabolites, whereas invasive cancers had significantly higher plasma cfDNA levels than all other groups. When stratified the supervised OPLS-DA analysis and total cfDNA concentration showed high discrimination accuracy between invasive cancers and the disease/medication-free subjects. Furthermore, comparison of OPLS-DA data for invasive breast cancers with the AIRWAVE cohort showed similar discrimination between breast cancers and healthy controls. This is the first report of agreement between metabolomics and plasma cfDNA levels for discriminating breast cancer from healthy subjects in a true screening population. It also emphasizes the importance of sample standardization. Follow on studies will involve analysis of candidate features in a larger validation series as well as comparing results with serial plasma samples taken at the next routine screening mammography appointment. The findings here help establish the role of plasma analysis in the diagnosis of breast cancer in a large real-world cohort.
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Affiliation(s)
- Justin Stebbing
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, Hammersmith, London, W12 0NN, UK
- School of Life Sciences, Faculty of Science and Engineering, ARU, East Road, Cambridge, CB1 1PT, UK
| | - Panteleimon G Takis
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK.
| | - Caroline J Sands
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | - Lynn Maslen
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | - Matthew R Lewis
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | - Kelly Gleason
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, Hammersmith, London, W12 0NN, UK
| | - Karen Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - David Guttery
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Daniel Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Lindsay Primrose
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Jacqueline A Shaw
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, Hammersmith, London, W12 0NN, UK
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
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Harshfield EL, Sands CJ, Tuladhar AM, de Leeuw FE, Lewis MR, Markus HS. Metabolomic profiling in small vessel disease identifies multiple associations with disease severity. Brain 2022; 145:2461-2471. [PMID: 35254405 PMCID: PMC9337813 DOI: 10.1093/brain/awac041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 05/13/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
Cerebral small vessel disease is a major cause of vascular cognitive impairment and dementia. There are few treatments, largely reflecting limited understanding of the underlying pathophysiology. Metabolomics can be used to identify novel risk factors to better understand pathogenesis and to predict disease progression and severity. We analysed data from 624 patients with symptomatic cerebral small vessel disease from two prospective cohort studies. Serum samples were collected at baseline and patients underwent MRI scans and cognitive testing at regular intervals with up to 14 years of follow-up. Using ultra-performance liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy, we obtained metabolic and lipidomic profiles from 369 annotated metabolites and 54 764 unannotated features and examined their association with respect to disease severity, assessed using MRI small vessel disease markers, cognition and future risk of all-cause dementia. Our analysis identified 28 metabolites that were significantly associated with small vessel disease imaging markers and cognition. Decreased levels of multiple glycerophospholipids and sphingolipids were associated with increased small vessel disease load as evidenced by higher white matter hyperintensity volume, lower mean diffusivity normalized peak height, greater brain atrophy and impaired cognition. Higher levels of creatine, FA(18:2(OH)) and SM(d18:2/24:1) were associated with increased lacune count, higher white matter hyperintensity volume and impaired cognition. Lower baseline levels of carnitines and creatinine were associated with higher annualized change in peak width of skeletonized mean diffusivity, and 25 metabolites, including lipoprotein subclasses, amino acids and xenobiotics, were associated with future dementia incidence. Our results show multiple distinct metabolic signatures that are associated with imaging markers of small vessel disease, cognition and conversion to dementia. Further research should assess causality and the use of metabolomic screening to improve the ability to predict future disease severity and dementia risk in small vessel disease. The metabolomic profiles may also provide novel insights into disease pathogenesis and help identify novel treatment approaches.
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Affiliation(s)
- Eric L Harshfield
- Correspondence to: Dr Eric L. Harshfield Stroke Research Group Department of Clinical Neurosciences University of Cambridge R3, Box 83, Cambridge Biomedical Campus Cambridge CB2 0QQ, UK E-mail:
| | - Caroline J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Anil M Tuladhar
- Department of Neurology, Donders Center for Medical Neuroscience, Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands
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Wilshaw J, Boswood A, Chang YM, Sands CJ, Camuzeaux S, Lewis MR, Xia D, Connolly DJ. Evidence of altered fatty acid metabolism in dogs with naturally occurring valvular heart disease and congestive heart failure. Metabolomics 2022; 18:34. [PMID: 35635592 PMCID: PMC9151558 DOI: 10.1007/s11306-022-01887-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/06/2022] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Myxomatous mitral valve disease (MMVD) is the most common cardiac condition in adult dogs. The disease progresses over several years and affected dogs may develop congestive heart failure (HF). Research has shown that myocardial metabolism is altered in cardiac disease, leading to a reduction in β-oxidation of fatty acids and an increased dependence upon glycolysis. OBJECTIVES This study aimed to evaluate whether a shift in substrate use occurs in canine patients with MMVD; a naturally occurring model of human disease. METHODS Client-owned dogs were longitudinally evaluated at a research clinic in London, UK and paired serum samples were selected from visits when patients were in ACVIM stage B1: asymptomatic disease without cardiomegaly, and stage C: HF. Samples were processed using ultra-performance liquid chromatography mass spectrometry and lipid profiles were compared using mixed effects models with false discovery rate adjustment. The effect of disease stage was evaluated with patient breed entered as a confounder. Features that significantly differed were screened for selection for annotation efforts using reference databases. RESULTS Dogs in HF had altered concentrations of lipid species belonging to several classes previously associated with cardiovascular disease. Concentrations of certain acylcarnitines, phospholipids and sphingomyelins were increased after individuals had developed HF, whilst some ceramides and lysophosphatidylcholines decreased. CONCLUSIONS The canine metabolome appears to change as MMVD progresses. Findings from this study suggest that in HF myocardial metabolism may be characterised by reduced β-oxidation. This proposed explanation warrants further research.
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Affiliation(s)
- Jenny Wilshaw
- Department of Clinical Science and Services, Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, London, United Kingdom.
| | - A Boswood
- Department of Clinical Science and Services, Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, London, United Kingdom
| | - Y M Chang
- Research Support Office, Royal Veterinary College, University of London, London, United Kingdom
| | - C J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - S Camuzeaux
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - M R Lewis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - D Xia
- Research Support Office, Royal Veterinary College, University of London, London, United Kingdom
- Department of Comparative Biomedical Science, Royal Veterinary College, University of London, London, United Kingdom
| | - D J Connolly
- Department of Clinical Science and Services, Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, London, United Kingdom
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Correia GDS, Takis PG, Sands CJ, Kowalka AM, Tan T, Turtle L, Ho A, Semple MG, Openshaw PJM, Baillie JK, Takáts Z, Lewis MR. 1H NMR Signals from Urine Excreted Protein Are a Source of Bias in Probabilistic Quotient Normalization. Anal Chem 2022; 94:6919-6923. [PMID: 35503092 PMCID: PMC9118196 DOI: 10.1021/acs.analchem.2c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/29/2022]
Abstract
Normalization to account for variation in urinary dilution is crucial for interpretation of urine metabolic profiles. Probabilistic quotient normalization (PQN) is used routinely in metabolomics but is sensitive to systematic variation shared across a large proportion of the spectral profile (>50%). Where 1H nuclear magnetic resonance (NMR) spectroscopy is employed, the presence of urinary protein can elevate the spectral baseline and substantially impact the resulting profile. Using 1H NMR profile measurements of spot urine samples collected from hospitalized COVID-19 patients in the ISARIC 4C study, we determined that PQN coefficients are significantly correlated with observed protein levels (r2 = 0.423, p < 2.2 × 10-16). This correlation was significantly reduced (r2 = 0.163, p < 2.2 × 10-16) when using a computational method for suppression of macromolecular signals known as small molecule enhancement spectroscopy (SMolESY) for proteinic baseline removal prior to PQN. These results highlight proteinuria as a common yet overlooked source of bias in 1H NMR metabolic profiling studies which can be effectively mitigated using SMolESY or other macromolecular signal suppression methods before estimation of normalization coefficients.
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Affiliation(s)
- Gonçalo D. S. Correia
- 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
- National
Phenome Centre, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, United Kingdom
- G. D. S. Correia.
| | - 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, United Kingdom
- National
Phenome Centre, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, United Kingdom
- P. G. Takis.
| | - 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, United Kingdom
- National
Phenome Centre, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, United Kingdom
| | - Anna M. Kowalka
- Division
of Diabetes, Endocrinology and Metabolism, Department of Metabolism,
Digestion and Reproduction, Imperial College
London, Du Cane Road, London W12 0NN, United Kingdom
- Clinical
Biochemistry, Blood Sciences, North West London Pathology, Charing Cross Hospital, London W6 8RF, United Kingdom
| | - Tricia Tan
- Division
of Diabetes, Endocrinology and Metabolism, Department of Metabolism,
Digestion and Reproduction, Imperial College
London, Du Cane Road, London W12 0NN, United Kingdom
- Clinical
Biochemistry, Blood Sciences, North West London Pathology, Charing Cross Hospital, London W6 8RF, United Kingdom
| | - Lance Turtle
- NIHR
Health Protection Research Unit in Emerging and Zoonotic Infections,
Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Antonia Ho
- MRC-University
of Glasgow Centre for Virus Research, University
of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Malcolm G. Semple
- NIHR
Health Protection Research Unit in Emerging and Zoonotic Infections,
Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, United Kingdom
- Respiratory
Medicine, Alder Hey Children’s Hospital, Liverpool L12 2AP, United Kingdom
| | - Peter J. M. Openshaw
- Faculty
of Medicine, National Heart and Lung Institute, Imperial College London, London SW3 6LY, United Kingdom
| | - J. Kenneth Baillie
- Roslin
Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Zoltán Takáts
- 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
- National
Phenome Centre, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, United Kingdom
| | - 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, United Kingdom
- National
Phenome Centre, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, United Kingdom
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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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Barnes DKA, Sands CJ, Paulsen ML, Moreno B, Moreau C, Held C, Downey R, Bax N, Stark JS, Zwerschke N. Correction to: Societal importance of Antarctic negative feedbacks on climate change: blue carbon gains from sea ice, ice shelf and glacier losses. Naturwissenschaften 2021; 108:51. [PMID: 34633554 DOI: 10.1007/s00114-021-01759-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - C J Sands
- British Antarctic Survey, NERC, Cambridge, UK
| | | | - B Moreno
- Universidad Científica del Sur, Lima, Peru
| | - C Moreau
- Université Libre de Bruxelles, Brussels, Belgium
| | - C Held
- Alfred Wegner Institute, Bremerhaven, Germany
| | - R Downey
- Australian National University, Canberra, Australia
| | - N Bax
- South Atlantic Environmental Research Institute, Stanley, South Atlantic, Falkland Islands
| | - J S Stark
- Australian Antarctic Division, Hobart, Australia
| | - N Zwerschke
- British Antarctic Survey, NERC, Cambridge, UK
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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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10
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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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11
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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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12
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Sands CJ, Wolfer AM, Correia GDS, Sadawi N, Ahmed A, Jiménez B, Lewis MR, Glen RC, Nicholson JK, Pearce JTM. The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets. Bioinformatics 2019; 35:5359-5360. [PMID: 31350543 PMCID: PMC6954639 DOI: 10.1093/bioinformatics/btz566] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 01/30/2019] [Revised: 06/18/2019] [Accepted: 07/19/2019] [Indexed: 12/24/2022] Open
Abstract
SUMMARY As large-scale metabolic phenotyping studies become increasingly common, the need for systemic methods for pre-processing and quality control (QC) of analytical data prior to statistical analysis has become increasingly important, both within a study, and to allow meaningful inter-study comparisons. The nPYc-Toolbox provides software for the import, pre-processing, QC and visualization of metabolic phenotyping datasets, either interactively, or in automated pipelines. AVAILABILITY AND IMPLEMENTATION The nPYc-Toolbox is implemented in Python, and is freely available from the Python package index https://pypi.org/project/nPYc/, source is available at https://github.com/phenomecentre/nPYc-Toolbox. Full documentation can be found at http://npyc-toolbox.readthedocs.io/ and exemplar datasets and tutorials at https://github.com/phenomecentre/nPYc-toolbox-tutorials.
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Affiliation(s)
- Caroline J Sands
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Arnaud M Wolfer
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Gonçalo D S Correia
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Noureddin Sadawi
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery & Cancer, Imperial College London, South Kensington, London, UK
| | - Arfan Ahmed
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Beatriz Jiménez
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery & Cancer, Imperial College London, South Kensington, London, UK
| | - Matthew R Lewis
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery & Cancer, Imperial College London, South Kensington, London, UK
| | - Robert C Glen
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery & Cancer, Imperial College London, South Kensington, London, UK
| | - Jeremy K Nicholson
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery & Cancer, Imperial College London, South Kensington, London, UK
| | - Jake T M Pearce
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Surgery & Cancer, Imperial College London, London, UK
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery & Cancer, Imperial College London, South Kensington, London, UK
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13
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Barnes DKA, Morley SA, Bell J, Brewin P, Brigden K, Collins M, Glass T, Goodall-Copestake WP, Henry L, Laptikhovsky V, Piechaud N, Richardson A, Rose P, Sands CJ, Schofield A, Shreeve R, Small A, Stamford T, Taylor B. Marine plastics threaten giant Atlantic Marine Protected Areas. Curr Biol 2019; 28:R1137-R1138. [PMID: 30300595 DOI: 10.1016/j.cub.2018.08.064] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
There has been a recent shift in global perception of plastics in the environment, resulting in a call for greater action. Science and the popular media have highlighted plastic as an increasing stressor [1,2]. Efforts have been made to confer protected status to some remote locations, forming some of the world's largest Marine Protected Areas, including several UK overseas territories. We assessed plastic at these remote Atlantic Marine Protected Areas, surveying the shore, sea surface, water column and seabed, and found drastic changes from 2013-2018. Working from the RRS James Clark Ross at Ascension, St. Helena, Tristan da Cunha, Gough and the Falkland Islands (Figure 1A), we showed that marine debris on beaches has increased more than 10 fold in the past decade. Sea surface plastics have also increased, with in-water plastics occurring at densities of 0.1 items m-3; plastics on seabeds were observed at ≤ 0.01 items m-2. For the first time, beach densities of plastics at remote South Atlantic sites approached those at industrialised North Atlantic sites. This increase even occurs hundreds of meters down on seamounts. We also investigated plastic incidence in 2,243 animals (comprising 26 species) across remote South Atlantic oceanic food webs, ranging from plankton to seabirds. We found that plastics had been ingested by primary consumers (zooplankton) to top predators (seabirds) at high rates. These findings suggest that MPA status will not mitigate the threat of plastic proliferation to this rich, unique and threatened biodiversity.
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Affiliation(s)
| | - S A Morley
- British Antarctic Survey, NERC, Cambridge, UK
| | - J Bell
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | - P Brewin
- South Atlantic Environment Research Institute, Stanley, Falkland Islands
| | - K Brigden
- South Atlantic Environment Research Institute, Stanley, Falkland Islands
| | - M Collins
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | - T Glass
- Tristan da Cunha Conservation Department, Edinburgh, UK Overseas Territory
| | | | - L Henry
- Marine Conservation, ENRD, St. Helena Government
| | - V Laptikhovsky
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | | | - A Richardson
- Ascension Island Conservation and Fisheries Department
| | - P Rose
- Pristine Seas, National Geographic Society, Washington DC, USA
| | - C J Sands
- British Antarctic Survey, NERC, Cambridge, UK
| | - A Schofield
- Royal Society for the Protection of Birds, Sandy, UK
| | - R Shreeve
- Marine Conservation, ENRD, St. Helena Government
| | - A Small
- Marine Conservation, ENRD, St. Helena Government
| | - T Stamford
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | - B Taylor
- St. Helena National Trust, Jamestown, St. Helena
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14
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Sands CJ, Coen M, Ebbels TMD, Holmes E, Lindon JC, Nicholson JK. Data-driven approach for metabolite relationship recovery in biological 1H NMR data sets using iterative statistical total correlation spectroscopy. Anal Chem 2011; 83:2075-82. [PMID: 21323345 DOI: 10.1021/ac102870u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Statistical total correlation spectroscopy (STOCSY) is a well-established and valuable method in the elucidation of both inter- and intrametabolite correlations in NMR metabonomic data sets. Here, the STOCSY approach is extended in a novel Iterative-STOCSY (I-STOCSY) tool in which correlations are calculated initially from a driver peak of interest and subsequently for all peaks identified as correlating with a correlation coefficient greater than a set threshold. Consequently, in a single automated run, the majority of information contained in multiple STOCSY calculations from all peaks recursively correlated to the original user defined driver peak of interest are recovered. In addition, highly correlating peaks are clustered into putative structurally related sets, and the results are presented in a fully interactive plot where each set is represented by a node; node-to-node connections are plotted alongside corresponding spectral data colored by the strength of connection, thus allowing the intuitive exploration of both inter- and intrametabolite connections. The I-STOCSY approach has been here applied to a (1)H NMR data set of 24 h postdose aqueous liver extracts from rats treated with the model hepatotoxin galactosamine and has been shown both to recover the previously deduced major metabolic effects of treatment and to generate new hypotheses even on this well-studied model system. I-STOCSY, thus, represents a significant advance in correlation based analysis and visualization, providing insight into inter- and intrametabolite relationships following metabolic perturbations.
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Affiliation(s)
- Caroline J Sands
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, SW7 2AZ, United Kingdom
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15
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Sands CJ, Coen M, Maher AD, Ebbels TMD, Holmes E, Lindon JC, Nicholson JK. Statistical Total Correlation Spectroscopy Editing of 1H NMR Spectra of Biofluids: Application to Drug Metabolite Profile Identification and Enhanced Information Recovery. Anal Chem 2009; 81:6458-66. [DOI: 10.1021/ac900828p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Caroline J. Sands
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Muireann Coen
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Anthony D. Maher
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Timothy M. D. Ebbels
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Elaine Holmes
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - John C. Lindon
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Jeremy K. Nicholson
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
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Garrick RC, Sands CJ, Rowell DM, Hillis DM, Sunnucks P. Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands - a multigene approach. Mol Ecol 2007; 16:1865-82. [PMID: 17444898 DOI: 10.1111/j.1365-294x.2006.03165.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phylogeography can reveal evolutionary processes driving natural genetic-geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long-term population history of a rotting-log-adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine-scale sampling combined with nested clade and coalescent-based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long-distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial-genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present-day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.
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Affiliation(s)
- R C Garrick
- Department of Genetics, La Trobe University, Bundoora, Vic. 3086, Australia.
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Garrick RC, Sands CJ, Rowell DM, Tait NN, Greenslade P, Sunnucks P. Phylogeography recapitulates topography: very fine-scale local endemism of a saproxylic ‘giant’ springtail at Tallaganda in the Great Dividing Range of south-east Australia. Mol Ecol 2004; 13:3329-44. [PMID: 15487993 DOI: 10.1111/j.1365-294x.2004.02340.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Comparative phylogeography can reveal processes and historical events that shape the biodiversity of species and communities. As part of a comparative research program, the phylogeography of a new, endemic Australian genus and species of log-dependent (saproxylic) collembola was investigated using mitochondrial sequences, allozymes and anonymous single-copy nuclear markers. We found the genetic structure of the species corresponds with five a priori microbiogeographical regions, with population subdivision at various depths owing to palaeoclimatic influences. Closely related mtDNA haplotypes are codistributed within a single region or occur in adjacent regions, nuclear allele frequencies are more similar among more proximate populations, and interpopulation migration is rare. Based on mtDNA divergence, a late Miocene-late Pliocene coalescence is likely. The present-day distribution of genetic diversity seems to have been impacted by three major climatic events: Pliocene cooling and drying (2.5-7 million years before present, Mybp), early Pleistocene wet-dry oscillations (c. 1.2 Mybp) and the more recent glacial-interglacial cycles that have characterized the latter part of the Quaternary (<0.4 Mybp).
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Affiliation(s)
- R C Garrick
- Department of Genetics and Evolution, Biological Sciences Building 1, La Trobe University, Plenty Road, Bundoora, VIC 3806, Australia.
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Abstract
This case demonstrates the use of the argon laser for ossicular mobilization. A preoperative audiologic evaluation revealed a severe conductive hearing loss, with a maximum air-bone gap. Since normal drilling procedures would result in a sensorineural hearing loss, the argon laser was chosen to remove a bony spur connecting the malleus to the posterior canal wall. When using the argon laser, no disarticulation of the incus and stapes is required. Postoperative audiologic evaluation revealed normal hearing sensitivity bilaterally.
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Affiliation(s)
- C J Sands
- Department of Surgery, University of New Mexico, Albuquerque
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Abstract
While toxic shock syndrome (TSS) is generally considered to be a tampon-related illness, an increasing number of reported cases have been related to surgical wounds. At least one case has been reported following nasal surgery with nasal packing. We report two additional cases of TSS associated with nasal packing. Because nasal packing is in some ways analogous to the use of tampons for menstrual hygiene, and nasal carriage of Staphylococcus aureus is frequent, the scarcity of TSS cases reported to occur following nasal packing is surprising. Otorhinolaryngologists are urged to report TSS cases associated with nasal packing to their state and local health departments or the Centers for Disease Control to aid in the understanding of the pathogenesis of this disease.
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Smith RO, Sands CJ, Goldberg NM, Massey RU, Gay JR. Injection of silicone lateral to a vocal cord in a patient with progressive bulbar palsy. Neurology 1967; 17:1217-8. [PMID: 6070024 DOI: 10.1212/wnl.17.12.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Sands CJ, Grossman J. A convenient sialogram catheter. Arch Otolaryngol 1966; 83:187. [PMID: 5902521 DOI: 10.1001/archotol.1966.00760020189023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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