1
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Gouveia GJ, Head T, Cheng LL, Clendinen CS, Cort JR, Du X, Edison AS, Fleischer CC, Hoch J, Mercaldo N, Pathmasiri W, Raftery D, Schock TB, Sumner LW, Takis PG, Copié V, Eghbalnia HR, Powers R. Perspective: use and reuse of NMR-based metabolomics data: what works and what remains challenging. Metabolomics 2024; 20:41. [PMID: 38480600 DOI: 10.1007/s11306-024-02090-6] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/12/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The National Cancer Institute issued a Request for Information (RFI; NOT-CA-23-007) in October 2022, soliciting input on using and reusing metabolomics data. This RFI aimed to gather input on best practices for metabolomics data storage, management, and use/reuse. AIM OF REVIEW The nuclear magnetic resonance (NMR) Interest Group within the Metabolomics Association of North America (MANA) prepared a set of recommendations regarding the deposition, archiving, use, and reuse of NMR-based and, to a lesser extent, mass spectrometry (MS)-based metabolomics datasets. These recommendations were built on the collective experiences of metabolomics researchers within MANA who are generating, handling, and analyzing diverse metabolomics datasets spanning experimental (sample handling and preparation, NMR/MS metabolomics data acquisition, processing, and spectral analyses) to computational (automation of spectral processing, univariate and multivariate statistical analysis, metabolite prediction and identification, multi-omics data integration, etc.) studies. KEY SCIENTIFIC CONCEPTS OF REVIEW We provide a synopsis of our collective view regarding the use and reuse of metabolomics data and articulate several recommendations regarding best practices, which are aimed at encouraging researchers to strengthen efforts toward maximizing the utility of metabolomics data, multi-omics data integration, and enhancing the overall scientific impact of metabolomics studies.
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Affiliation(s)
- Goncalo Jorge Gouveia
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA
| | - Thomas Head
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Leo L Cheng
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Pathology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chaevien S Clendinen
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - John R Cort
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Earth and Biological Sciences Directorate, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xiuxia Du
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9291 University City Blvd, Charlotte, NC, 28223, USA
| | - Arthur S Edison
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Biochemistry, University of Georgia, Athens, GA, USA
| | - Candace C Fleischer
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeffrey Hoch
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06030-3305, USA
| | - Nathaniel Mercaldo
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wimal Pathmasiri
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Nutrition, School of Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Daniel Raftery
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Anesthesia and Pain Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Tracey B Schock
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Lloyd W Sumner
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Biochemistry, MU Metabolomics Center, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - Panteleimon G Takis
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW7 2AZ, UK
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - Valérie Copié
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Hamid R Eghbalnia
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06030-3305, USA
| | - Robert Powers
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada.
- Department of Chemistry, Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE, 68588-0304, USA.
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2
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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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4
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Harvey N, Takis PG, Lindon JC, Li JV, Jiménez B. Optimization of Diffusion-Ordered NMR Spectroscopy Experiments for High-Throughput Automation in Human Metabolic Phenotyping. Anal Chem 2023; 95:3147-3152. [PMID: 36720172 PMCID: PMC9933041 DOI: 10.1021/acs.analchem.2c04066] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/19/2023] [Indexed: 02/02/2023]
Abstract
The diffusion-ordered nuclear magnetic resonance spectroscopy (DOSY) experiment allows the calculation of diffusion coefficient values of metabolites in complex mixtures. However, this experiment has not yet been broadly used for metabolic profiling due to lack of a standardized protocol. Here we propose a pipeline for the DOSY experimental setup and data processing in metabolic phenotyping studies. Due to the complexity of biological samples, three experiments (a standard DOSY, a relaxation-edited DOSY, and a diffusion-edited DOSY) have been optimized to provide DOSY metabolic profiles with peak-picked diffusion coefficients for over 90% of signals visible in the one-dimensional 1H general biofluid profile in as little as 3 min 36 s. The developed parameter sets and tools are straightforward to implement and can facilitate the use of DOSY for metabolic profiling of human blood plasma and urine samples.
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Affiliation(s)
- Nikita Harvey
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, Burlington Danes Building, Hammersmith Hospital Campus, London W12 0NN, U.K.
- National
Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, , IRDB Building, Hammersmith
Campus, London W12 0NN, U.K.
| | - Panteleimon G Takis
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, Burlington Danes Building, Hammersmith Hospital Campus, London W12 0NN, U.K.
- National
Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, , IRDB Building, Hammersmith
Campus, London W12 0NN, U.K.
| | - John C Lindon
- Section
of Biomolecular Medicine, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, Burlington Danes Building, Hammersmith Hospital Campus, London W12 0NN, U.K.
| | - Jia V Li
- Section
of Nutrition, Division of Digestive Diseases, Department of Metabolism,
Digestion and Reproduction, Imperial College
London, Commonwealth Building, Hammersmith Hospital Campus, London W12 0NN, U.K.
| | - Beatriz Jiménez
- Section
of Bioanalytical Chemistry, Division of Systems Medicine, Department
of Metabolism, Digestion and Reproduction, Imperial College London, Burlington Danes Building, Hammersmith Hospital Campus, London W12 0NN, U.K.
- National
Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, , IRDB Building, Hammersmith
Campus, London W12 0NN, U.K.
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5
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Takis PG, Vuckovic I, Tan T, Denic A, Lieske JC, Lewis MR, Macura S. NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles. Bioinformatics 2022; 38:4437-4439. [PMID: 35861573 PMCID: PMC9477529 DOI: 10.1093/bioinformatics/btac502] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY 1H nuclear magnetic resonance (NMR) spectroscopy is an established bioanalytical technology for metabolic profiling of biofluids in both clinical and large-scale population screening applications. Recently, urinary protein quantification has been demonstrated using the same 1D 1H NMR experimental data captured for metabolic profiling. Here, we introduce NMRpQuant, a freely available platform that builds on these findings with both novel and further optimized computational NMR approaches for rigorous, automated protein urine quantification. The results are validated by interlaboratory comparisons, demonstrating agreement with clinical/biochemical methodologies, pointing at a ready-to-use tool for routine protein urinalyses. AVAILABILITY AND IMPLEMENTATION NMRpQuant was developed on MATLAB programming environment. Source code and Windows/macOS compiled applications are available at https://github.com/pantakis/NMRpQuant, and working examples are available at https://doi.org/10.6084/m9.figshare.18737189.v1. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ivan Vuckovic
- Metabolomics Core, Mayo Clinic, Rochester, MN 55905, USA
| | - Tricia Tan
- Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK,Clinical Biochemistry, Blood Sciences, North West London Pathology, Charing Cross Hospital, London W6 8RF, UK
| | - Aleksandar Denic
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew R Lewis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK,National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK
| | - Slobodan Macura
- Metabolomics Core, Mayo Clinic, Rochester, MN 55905, USA,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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6
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Chasapi SA, Karagkouni E, Kalavrizioti D, Vamvakas S, Zompra A, Takis PG, Goumenos DS, Spyroulias GA. NMR-Based Metabolomics in Differential Diagnosis of Chronic Kidney Disease (CKD) Subtypes. Metabolites 2022; 12:metabo12060490. [PMID: 35736423 PMCID: PMC9230636 DOI: 10.3390/metabo12060490] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 02/01/2023] Open
Abstract
Chronic Kidney Disease (CKD) is considered as a major public health problem as it can lead to end-stage kidney failure, which requires replacement therapy. A prompt and accurate diagnosis, along with the appropriate treatment, can delay CKD’s progression, significantly. Herein, we sought to determine whether CKD etiology can be reflected in urine metabolomics during its early stage. This is achieved through the analysis of the urine metabolic fingerprint from 108 CKD patients by means of Nuclear Magnetic Resonance (NMR) spectroscopy metabolomic analysis. We report the first NMR—metabolomics data regarding the three most common etiologies of CKD: Chronic Glomerulonephritis (IgA and Membranous Nephropathy), Diabetic Nephropathy (DN) and Hypertensive Nephrosclerosis (HN). Analysis aided a moderate glomerulonephritis clustering, providing characterization of the metabolic fluctuations between the CKD subtypes and control disease. The urine metabolome of IgA Nephropathy reveals a specific metabolism, reflecting its different etiology or origin and is useful for determining the origin of the disease. In contrast, urine metabolomes from DN and HN patients did not reveal any indicative metabolic pattern, which is consistent with their fused clinical phenotype. These findings may contribute to improving diagnostics and prognostic approaches for CKD, as well as improving our understanding of its pathology.
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Affiliation(s)
- Styliani A. Chasapi
- Department of Pharmacy, University of Patras, 26504 Patras, Greece; (S.A.C.); (E.K.); (A.Z.)
| | - Evdokia Karagkouni
- Department of Pharmacy, University of Patras, 26504 Patras, Greece; (S.A.C.); (E.K.); (A.Z.)
| | - Dimitra Kalavrizioti
- Department of Nephrology and Renal Transplantation, University Hospital of Patras, 26504 Patras, Greece; (D.K.); (S.V.)
| | - Sotirios Vamvakas
- Department of Nephrology and Renal Transplantation, University Hospital of Patras, 26504 Patras, Greece; (D.K.); (S.V.)
| | - Aikaterini Zompra
- Department of Pharmacy, University of Patras, 26504 Patras, Greece; (S.A.C.); (E.K.); (A.Z.)
| | - 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 W120NN, UK
| | - Dimitrios S. Goumenos
- Department of Nephrology and Renal Transplantation, University Hospital of Patras, 26504 Patras, Greece; (D.K.); (S.V.)
- Correspondence: (D.S.G.); (G.A.S.)
| | - Georgios A. Spyroulias
- Department of Pharmacy, University of Patras, 26504 Patras, Greece; (S.A.C.); (E.K.); (A.Z.)
- Correspondence: (D.S.G.); (G.A.S.)
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7
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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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8
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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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9
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Donisi G, Barbagallo M, Capretti G, Nappo G, Takis PG, Zerbi A, Marchesi F, Cortese N. Isolation of Proximal Fluids to Investigate the Tumor Microenvironment of Pancreatic Adenocarcinoma. J Vis Exp 2020. [PMID: 33226019 DOI: 10.3791/61687] [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: 10/31/2022] Open
Abstract
Pancreatic adenocarcinoma (PDAC) is the fourth leading cause of cancer-related death, and soon to become the second. There is an urgent need of variables associated to specific pancreatic pathologies to help preoperative differential diagnosis and patient profiling. Pancreatic juice is a relatively unexplored body fluid, which, due to its close proximity to the tumor site, reflects changes in the surrounding tissue. Here we describe in detail the intraoperative collection procedure. Unfortunately, translating pancreatic juice collection to murine models of PDAC, to perform mechanistic studies, is technically very challenging. Tumor interstitial fluid (TIF) is the extracellular fluid, outside blood and plasma, which bathes tumor and stromal cells. Similarly to pancreatic juice, for its property to collect and concentrate molecules that are found diluted in plasma, TIF can be exploited as an indicator of microenvironmental alterations and as a valuable source of disease-associated biomarkers. Since TIF is not readily accessible, various techniques have been proposed for its isolation. We describe here two simple and technically undemanding methods for its isolation: tissue centrifugation and tissue elution.
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Affiliation(s)
- Greta Donisi
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS
| | - Marialuisa Barbagallo
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS
| | - Giovanni Capretti
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS; Department of Biomedical Sciences, Humanitas University
| | - Gennaro Nappo
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS; Department of Biomedical Sciences, Humanitas University
| | - Panteleimon G Takis
- Giotto Biotech S.R.L.; Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London; National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London
| | - Alessandro Zerbi
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS; Department of Biomedical Sciences, Humanitas University
| | - Federica Marchesi
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS; Department of Medical Biotechnology and Translational Medicine, University of Milan;
| | - Nina Cortese
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS;
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10
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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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11
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Musio B, Ragone R, Todisco S, Rizzuti A, Latronico M, Mastrorilli P, Pontrelli S, Intini N, Scapicchio P, Triggiani M, Di Noia T, Acquotti D, Airoldi C, Assfalg M, Barge A, Bateman L, Benevelli F, Bertelli D, Bertocchi F, Bieliauskas A, Borioni A, Caligiani A, Callone E, Čamra A, Cesare Marincola F, Chalasani D, Consonni R, Dambruoso P, Davalli S, David T, Diehl B, Donarski J, Gil AM, Gobetto R, Goldoni L, Hamon E, Harwood JS, Kobrlová A, Longobardi F, Luisi R, Mallamace D, Mammi S, Martin-Biran M, Mazzei P, Mele A, Milone S, Molero Vilchez D, Mulder RJ, Napoli C, Ragno D, Randazzo A, Rossi MC, Rotondo A, Šačkus A, Sáez Barajas E, Schievano E, Sitaram B, Stevanato L, Takis PG, Teipel J, Thomas F, Torregiani E, Valensin D, Veronesi M, Warren J, Wist J, Zailer-Hafer E, Zuccaccia C, Gallo V. A community-built calibration system: The case study of quantification of metabolites in grape juice by qNMR spectroscopy. Talanta 2020; 214:120855. [PMID: 32278434 DOI: 10.1016/j.talanta.2020.120855] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
Nuclear Magnetic Resonance (NMR) is an analytical technique extensively used in almost every chemical laboratory for structural identification. This technique provides statistically equivalent signals in spite of using spectrometer with different hardware features and is successfully used for the traceability and quantification of analytes in food samples. Nevertheless, to date only a few internationally agreed guidelines have been reported on the use of NMR for quantitative analysis. The main goal of the present study is to provide a methodological pipeline to assess the reproducibility of NMR data produced for a given matrix by spectrometers from different manufacturers, with different magnetic field strengths, age and hardware configurations. The results have been analyzed through a sequence of chemometric tests to generate a community-built calibration system which was used to verify the performance of the spectrometers and the reproducibility of the predicted sample concentrations.
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Affiliation(s)
- Biagia Musio
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy.
| | - Rosa Ragone
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy; Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy
| | - Stefano Todisco
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy; Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy
| | - Antonino Rizzuti
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy; Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy
| | - Mario Latronico
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy; Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy
| | - Piero Mastrorilli
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy; Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy
| | - Stefania Pontrelli
- Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy
| | - Nicola Intini
- Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy; Agenzia Regionale per la Prevenzione e la Protezione dell'Ambiente, ARPA Puglia, Corso Trieste 127, I-70126, Bari, Italy
| | - Pasquale Scapicchio
- SAMER (Special Agency of the Chamber of Commerce of Bari), Via E. Mola 19, I-70121, Bari, Italy; RETELAB (Italian Network of the laboratories of the Chambers of Commerce) and LACHIMER (Special Agency of the Chamber of Commerce of Foggia), Via Manfredonia Km 2,200, I-71121, Foggia, Italy
| | - Maurizio Triggiani
- Dipartimento di Ingegneria Elettrica e dell'Informazione, Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy
| | - Tommaso Di Noia
- Dipartimento di Ingegneria Elettrica e dell'Informazione, Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy
| | - Domenico Acquotti
- Centro Inter-dipartimentale Misure (CIM), Università degli Studi di Parma, Parco Area delle Scienze 23/A, I-43124, Parma, Italy
| | - Cristina Airoldi
- Dipartimento di Biotecnologie e Bioscienze, Università of Milano-Bicocca, P.zza della Scienza 2, I-20126, Milano, Italy
| | - Michael Assfalg
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Cà Vignal 1, Strada le Grazie 15, I-37134, Verona, Italy
| | - Alessandro Barge
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Verdi 8, 10124, Torino, Italy
| | - Lorraine Bateman
- School of Chemistry and School of Pharmacy, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College Cork, T12 K8AF, Ireland
| | - Francesca Benevelli
- Bruker Italia S.r.l., Viale V. Lancetti 43, I-20158, Milano, Italy; 7C-Consortium for NMR Research in Biotechnology and Material Science, Via Colombo 81, I-20133, Milano, Italy
| | - Davide Bertelli
- Dipartimento Scienze della Vita, Università di Modena e Reggio Emilia, Via campi 103, 41125, Modena, Italy
| | - Fabio Bertocchi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Via della Ricerca Scientifica, 00133, Roma, Italy
| | - Aurimas Bieliauskas
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko Str. 59, LT-51423, Kaunas, Lithuania
| | - Anna Borioni
- Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, I-00161, Roma, Italy
| | - Augusta Caligiani
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124, Parma, Italy
| | - Emanuela Callone
- "K. Müller" Magnetic Resonance Lab., Dipartimento di Ingegneria Industriale, Università di Trento, Via Sommarive 9, 38123, Trento (TN), Italy
| | - Ales Čamra
- General Directorate of Customs, Budějovická 7, 140 00, Prague, Czech Republic
| | - Flaminia Cesare Marincola
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato SS 554, I-09012 Monserrato (CA), Italy
| | - Dinesh Chalasani
- The United States Pharmacopeial Convention (USP), 12601 Twinbrook Parkway, Rockville, MD, 20852-1790, USA
| | - Roberto Consonni
- Istituto per lo Studio delle Macromolecole del Consiglio Nazionale delle Ricerche, (ISMAC-CNR), Laboratorio NMR, Via Bassini 15, I-20133, Milano, Italy
| | - Paolo Dambruoso
- Istituto per la Sintesi Organica e la Fotoreattività del Consiglio Nazionale delle Ricerche (ISOF-CNR), Via P. Gobetti 101, 40129 Bologna, Italy
| | - Silvia Davalli
- Aptuit (Verona) S.r.l., Via Fleming 4, I-37135, Verona, Italy
| | - Taylor David
- The United States Pharmacopeial Convention (USP), 12601 Twinbrook Parkway, Rockville, MD, 20852-1790, USA
| | - Bernd Diehl
- Spectral Service AG, Emil-Hoffmann-Straße 33, 50996, Köln, Germany
| | - James Donarski
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Ana M Gil
- CICECO - Aveiro Institute of Materials, Department of Chemistry, Campus Universitario de Santiago, University of Aveiro, 3810-093, Aveiro, Portugal
| | - Roberto Gobetto
- Dipartimento di Chimica, Università degli Studi di Torino, Via Pietro Giuria 7, 10125, Torino, Italy
| | - Luca Goldoni
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genova, Italy
| | - Erwann Hamon
- Aérial, 250 Rue Laurent Fries - CS40443, 67412, Illkirch Cedex, France
| | - John S Harwood
- Purdue Interdepartmental NMR Facility, Weatherill Laboratory Room 365B 560, Oval Drive, West Lafayette, IN 47907-2084, Indiana, USA
| | - Andrea Kobrlová
- General Directorate of Customs, Budějovická 7, 140 00, Prague, Czech Republic
| | - Francesco Longobardi
- Dipartimento di Chimica, Università degli Studi di Bari "A. Moro", Via Orabona 4, I-70125, Bari, Italy
| | - Renzo Luisi
- Department of Pharmacy - Drug Sciences, University of Bari "A. Moro", FLAME-Lab - Flow Chemistry and Microreactor Technology Laboratory, Via E. Orabona 4, 70125, Bari, Italy
| | - Domenico Mallamace
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, I-98166, Messina, Italy
| | - Stefano Mammi
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, I-35100, Padova, Italy
| | - Magali Martin-Biran
- Ctre Recherche Valorisation Application (CEREVAA), 12 Allée ISAAC NEWTON, 33650, Martillac, France
| | - Pierluigi Mazzei
- Università di Napoli Federico II, Centro Interdipartimentale di Risonanza Magnetica Nucleare (CERMANU), Via Università 100, 80055, Portici, Italy
| | - Andrea Mele
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza L. da Vinci 32, 20133, Milano, Italy
| | - Salvatore Milone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Campo Boario, I-64100, Teramo, Italy
| | - Dolores Molero Vilchez
- Universidad Complutense de Madrid, Avda. Complutense s/n Aulario Facultad de Quimicas, 28040, Madrid, Spain
| | | | - Claudia Napoli
- Bruker Italia S.r.l., Viale V. Lancetti 43, I-20158, Milano, Italy
| | - Daniele Ragno
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Via L. Borsari 46, I-44121, Ferrara, Italy
| | - Antonio Randazzo
- Dipartimento di Farmacia, Università di Napoli, Via D. Montesano, 80131, Napoli, Italy
| | - Maria Cecilia Rossi
- Centro Interdipartimentale Grandi Strumenti (CIGS), Università di Modena e Reggio Emilia, Via G. Campi 213/A, 41125, Modena, Italy
| | - Archimede Rotondo
- Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Piazza Pugliatti 1, 98122, Messina, Italy; Science4life s.r.l., Via Leonardo Sciascia Coop. Fede Pal.B, 98168, Messina, Italy
| | - Algirdas Šačkus
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko Str. 59, LT-51423, Kaunas, Lithuania
| | - Elena Sáez Barajas
- Universidad Complutense de Madrid, Avda. Complutense s/n Aulario Facultad de Quimicas, 28040, Madrid, Spain
| | - Elisabetta Schievano
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, I-35100, Padova, Italy
| | - Bhavaraju Sitaram
- The United States Pharmacopeial Convention (USP), 12601 Twinbrook Parkway, Rockville, MD, 20852-1790, USA
| | - Livio Stevanato
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Verdi 8, 10124, Torino, Italy
| | - Panteleimon G Takis
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine - CERM/CIRMMP, Via Luigi Sacconi 6, I-50019, Sesto Fiorentino (FI), Italy
| | - Jan Teipel
- Chemical and Veterinary Investigation Agency of East-Westphalia-Lippe, Westerfeldstraße 1, 32758, Detmold, Germany
| | - Freddy Thomas
- Eurofins Analytics France, 9 Rue P. A. Bobierre, BP42301, 44323, Nantes, France
| | - Elisabetta Torregiani
- Dipartimento di Scienze Chimiche, Università di Camerino, Via S. Agostino 1, 62032, Camerino, Italy
| | - Daniela Valensin
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Marina Veronesi
- D3-PharmaChemistry, Fondazione Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genova, Italy
| | - John Warren
- LGC Limited, Queen's Road, TW11 0LY, Teddington, United Kingdom
| | - Julien Wist
- Departamento de Quimica, Universidad del Valle, Calle 13 No 100-00, Cali, Colombia
| | | | - Cristiano Zuccaccia
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia and CIRCC, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Vito Gallo
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di Chimica (DICATECh), Politecnico di Bari, Via Orabona 4, I-70125, Bari, Italy; Innovative Solutions S.r.l, Spin Off del Politecnico di Bari, Zona H 150/B, I-70015, Noci (BA), Italy; SAMER (Special Agency of the Chamber of Commerce of Bari), Via E. Mola 19, I-70121, Bari, Italy.
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12
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Cortese N, Capretti G, Barbagallo M, Rigamonti A, Takis PG, Castino GF, Vignali D, Maggi G, Gavazzi F, Ridolfi C, Nappo G, Donisi G, Erreni M, Avigni R, Rahal D, Spaggiari P, Roncalli M, Cappello P, Novelli F, Monti P, Zerbi A, Allavena P, Mantovani A, Marchesi F. Metabolome of Pancreatic Juice Delineates Distinct Clinical Profiles of Pancreatic Cancer and Reveals a Link between Glucose Metabolism and PD-1 + Cells. Cancer Immunol Res 2020; 8:493-505. [PMID: 32019781 DOI: 10.1158/2326-6066.cir-19-0403] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 11/16/2022]
Abstract
Better understanding of pancreatic diseases, including pancreatic ductal adenocarcinoma (PDAC), is an urgent medical need, with little advances in preoperative differential diagnosis, preventing rational selection of therapeutic strategies. The clinical management of pancreatic cancer patients would benefit from the identification of variables distinctively associated with the multiplicity of pancreatic disorders. We investigated, by 1H nuclear magnetic resonance, the metabolomic fingerprint of pancreatic juice (the biofluid that collects pancreatic products) in 40 patients with different pancreatic diseases. Metabolic variables discriminated PDAC from other less aggressive pancreatic diseases and identified metabolic clusters of patients with distinct clinical behaviors. PDAC specimens were overtly glycolytic, with significant accumulation of lactate, which was probed as a disease-specific variable in pancreatic juice from a larger cohort of 106 patients. In human PDAC sections, high expression of the glucose transporter GLUT-1 correlated with tumor grade and a higher density of PD-1+ T cells, suggesting their accumulation in glycolytic tumors. In a preclinical model, PD-1+ CD8 tumor-infiltrating lymphocytes differentially infiltrated PDAC tumors obtained from cell lines with different metabolic consumption, and tumors metabolically rewired by knocking down the phosphofructokinase (Pfkm) gene displayed a decrease in PD-1+ cell infiltration. Collectively, we introduced pancreatic juice as a valuable source of metabolic variables that could contribute to differential diagnosis. The correlation of metabolic markers with immune infiltration suggests that upfront evaluation of the metabolic profile of PDAC patients could foster the introduction of immunotherapeutic approaches for pancreatic cancer.
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Affiliation(s)
- Nina Cortese
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Giovanni Capretti
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele-Milan, Italy
| | - Marialuisa Barbagallo
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Alessandra Rigamonti
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Panteleimon G Takis
- Giotto Biotech S.R.L., Sesto Fiorentino, Florence, Italy.,Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Giovanni F Castino
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Debora Vignali
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giulia Maggi
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Francesca Gavazzi
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Cristina Ridolfi
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Gennaro Nappo
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Greta Donisi
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Marco Erreni
- Unit of Advanced Optical Microscopy, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Roberta Avigni
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Daoud Rahal
- Department of Pathology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Paola Spaggiari
- Department of Pathology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Massimo Roncalli
- Humanitas University, Department of Biomedical Sciences, Pieve Emanuele-Milan, Italy.,Department of Pathology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Paola Cappello
- Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino and Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Francesco Novelli
- Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino and Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Paolo Monti
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Alessandro Zerbi
- Section of Pancreatic Surgery, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele-Milan, Italy
| | - Paola Allavena
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Alberto Mantovani
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.,Humanitas University, Department of Biomedical Sciences, Pieve Emanuele-Milan, Italy.,The William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Federica Marchesi
- Department of Immunology and Inflammation, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy. .,Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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13
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Abstract
Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.
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Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P.Via Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Veronica Ghini
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Gaia Meoni
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Cristina Licari
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of FlorenceLargo Brambilla 3FlorenceItaly
| | - Paola Turano
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| | - Claudio Luchinat
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
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14
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Vignoli A, Tenori L, Giusti B, Takis PG, Valente S, Carrabba N, Balzi D, Barchielli A, Marchionni N, Gensini GF, Marcucci R, Luchinat C, Gori AM. NMR-based metabolomics identifies patients at high risk of death within two years after acute myocardial infarction in the AMI-Florence II cohort. BMC Med 2019; 17:3. [PMID: 30616610 PMCID: PMC6323789 DOI: 10.1186/s12916-018-1240-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Risk stratification and management of acute myocardial infarction patients continue to be challenging despite considerable efforts made in the last decades by many clinicians and researchers. The aim of this study was to investigate the metabolomic fingerprint of acute myocardial infarction using nuclear magnetic resonance spectroscopy on patient serum samples and to evaluate the possible role of metabolomics in the prognostic stratification of acute myocardial infarction patients. METHODS In total, 978 acute myocardial infarction patients were enrolled in this study; of these, 146 died and 832 survived during 2 years of follow-up after the acute myocardial infarction. Serum samples were analyzed via high-resolution 1H-nuclear magnetic resonance spectroscopy and the spectra were used to characterize the metabolic fingerprint of patients. Multivariate statistics were used to create a prognostic model for the prediction of death within 2 years after the cardiovascular event. RESULTS In the training set, metabolomics showed significant differential clustering of the two outcomes cohorts. A prognostic risk model predicted death with 76.9% sensitivity, 79.5% specificity, and 78.2% accuracy, and an area under the receiver operating characteristics curve of 0.859. These results were reproduced in the validation set, obtaining 72.6% sensitivity, 72.6% specificity, and 72.6% accuracy. Cox models were used to compare the known prognostic factors (for example, Global Registry of Acute Coronary Events score, age, sex, Killip class) with the metabolomic random forest risk score. In the univariate analysis, many prognostic factors were statistically associated with the outcomes; among them, the random forest score calculated from the nuclear magnetic resonance data showed a statistically relevant hazard ratio of 6.45 (p = 2.16×10-16). Moreover, in the multivariate regression only age, dyslipidemia, previous cerebrovascular disease, Killip class, and random forest score remained statistically significant, demonstrating their independence from the other variables. CONCLUSIONS For the first time, metabolomic profiling technologies were used to discriminate between patients with different outcomes after an acute myocardial infarction. These technologies seem to be a valid and accurate addition to standard stratification based on clinical and biohumoral parameters.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine - C.I.R.M.M.P, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy. .,Careggi Hospital, Florence, Italy.
| | | | | | | | | | | | - Niccolò Marchionni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Careggi Hospital, Florence, Italy
| | | | - Rossella Marcucci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Careggi Hospital, Florence, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine - C.I.R.M.M.P, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Gori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Careggi Hospital, Florence, Italy
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15
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Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P. Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Veronica Ghini
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Gaia Meoni
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Cristina Licari
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of Florence Largo Brambilla 3 Florence Italien
| | - Paola Turano
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| | - Claudio Luchinat
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
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16
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Takis PG, Taddei A, Pini R, Grifoni S, Tarantini F, Bechi P, Luchinat C. Fingerprinting Acute Digestive Diseases by Untargeted NMR Based Metabolomics. Int J Mol Sci 2018; 19:ijms19113288. [PMID: 30360494 PMCID: PMC6274841 DOI: 10.3390/ijms19113288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/18/2022] Open
Abstract
Precision medicine may significantly contribute to rapid disease diagnosis and targeted therapy, but relies on the availability of detailed, subject specific, clinical information. Proton nuclear magnetic resonance (1H–NMR) spectroscopy of body fluids can extract individual metabolic fingerprints. Herein, we studied 64 patients admitted to the Florence main hospital emergency room with severe abdominal pain. A blood sample was drawn from each patient at admission, and the corresponding sera underwent 1H–NMR metabolomics fingerprinting. Unsupervised Principal Component Analysis (PCA) analysis showed a significant discrimination between a group of patients with symptoms of upper abdominal pain and a second group consisting of patients with diffuse abdominal/intestinal pain. Prompted by this observation, supervised statistical analysis (Orthogonal Partial Least Squares–Discriminant Analysis (OPLS-DA)) showed a very good discrimination (>90%) between the two groups of symptoms. This is a surprising finding, given that neither of the two symptoms points directly to a specific disease among those studied here. Actually herein, upper abdominal pain may result from either symptomatic gallstones, cholecystitis, or pancreatitis, while diffuse abdominal/intestinal pain may result from either intestinal ischemia, strangulated obstruction, or mechanical obstruction. Although limited by the small number of samples from each of these six conditions, discrimination of these diseases was attempted. In the first symptom group, >70% discrimination accuracy was obtained among symptomatic gallstones, pancreatitis, and cholecystitis, while for the second symptom group >85% classification accuracy was obtained for intestinal ischemia, strangulated obstruction, and mechanical obstruction. No single metabolite stands up as a possible biomarker for any of these diseases, while the contribution of the whole 1H–NMR serum fingerprint seems to be a promising candidate, to be confirmed on larger cohorts, as a first-line discriminator for these diseases.
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Affiliation(s)
- Panteleimon G Takis
- Giotto Biotech, S.r.l, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Antonio Taddei
- Department of Surgery and Translational Medicine, School of Medicine, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy.
| | - Riccardo Pini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy.
| | - Stefano Grifoni
- Department of Emergency Medicine and Surgery, Careggi University Hospital, 50134 Florence, Italy.
| | - Francesca Tarantini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy.
| | - Paolo Bechi
- Department of Surgery and Translational Medicine, School of Medicine, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy.
| | - Claudio Luchinat
- Giotto Biotech, S.r.l, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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17
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Panteleimon G. Takis
- Giotto Biotech S.R.L.; Via Madonna del Piano 6 50019 Sesto Fiorentino (FI) Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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18
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Takis PG, Schäfer H, Spraul M, Luchinat C. Deconvoluting interrelationships between concentrations and chemical shifts in urine provides a powerful analysis tool. Nat Commun 2017; 8:1662. [PMID: 29162796 PMCID: PMC5698486 DOI: 10.1038/s41467-017-01587-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/29/2017] [Indexed: 02/08/2023] Open
Abstract
The NMR chemical shifts of a substance in a complex mixture strongly depend on the composition of the mixture itself, as many weak interactions occur that are hardly predictable. Chemical shift variability is the major obstacle to automatically assigning, and subsequently quantitating, metabolite signals in body fluids, particularly urine. Here we demonstrate that the chemical shifts of signals in urine are actually predictable. This is achieved by constructing ca. 4000 artificial mixtures where the concentrations of 52 most abundant urine metabolites-including 11 inorganic ions-are varied, to sparsely but efficiently populate an N-dimensional concentration matrix. A strong relationship is established between the concentration matrix and the chemical shift matrix, so that chemical shifts of > 90 metabolite signals can be accurately predicted in real urine samples. The concentrations of the invisible inorganic ions are also accurately predicted, along with those of albumin and of several other abundant urine components.
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Affiliation(s)
- Panteleimon G Takis
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Hartmut Schäfer
- Bruker BioSpin, Silberstreifen, D-76287, Rheinstetten, Germany
| | - Manfred Spraul
- Bruker BioSpin, Silberstreifen, D-76287, Rheinstetten, Germany
| | - Claudio Luchinat
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy.
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.
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19
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Takis PG, Tenori L, Ravera E, Luchinat C. Gelified Biofluids for High-Resolution Magic Angle Spinning 1H NMR Analysis: The Case of Urine. Anal Chem 2017; 89:1054-1058. [DOI: 10.1021/acs.analchem.6b04318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Panteleimon G. Takis
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Leonardo Tenori
- Department
of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
- Magnetic
Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi
6, 50019 Sesto Fiorentino, Florence, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi
6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Florence, Italy
- Magnetic
Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi
6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
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20
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Takis PG, Papavasileiou KD, Peristeras LD, Boulougouris GC, Melissas VS, Troganis AN. Unscrambling micro-solvation of –COOH and –NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies. Phys Chem Chem Phys 2017; 19:13710-13722. [DOI: 10.1039/c7cp01592e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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
This study investigates the interactions of –COOH and –NH groups in neat DMSO solutions, with special focus on their thermodynamics and kinetics.
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Affiliation(s)
- Panteleimon G. Takis
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
| | - Konstantinos D. Papavasileiou
- National Center for Scientific Research “Demokritos”
- Institute of Nanoscience and Nanotechnology
- Molecular Thermodynamics and Modelling of Materials Laboratory (MTMML)
- GR-153 10 Aghia Paraskevi Attikis
- Greece
| | - Loukas D. Peristeras
- National Center for Scientific Research “Demokritos”
- Institute of Nanoscience and Nanotechnology
- Molecular Thermodynamics and Modelling of Materials Laboratory (MTMML)
- GR-153 10 Aghia Paraskevi Attikis
- Greece
| | - Georgios C. Boulougouris
- Department of Molecular Biology and Genetics
- Democritus University of Thrace
- GR-681 00 Alexandroupolis
- Greece
| | | | - Anastassios N. Troganis
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
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21
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Takis PG, Oraiopoulou ME, Konidaris C, Troganis AN. 1H-NMR based metabolomics study for the detection of the human urine metabolic profile effects of Origanum dictamnus tea ingestion. Food Funct 2016; 7:4104-15. [DOI: 10.1039/c6fo00560h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR based metabolomics clarify theOriganum dictamnustea effect upon the human urine metabolome.
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Affiliation(s)
- Panteleimon G. Takis
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
| | - Mariam-Eleni Oraiopoulou
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
| | - Constantinos Konidaris
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
| | - Anastassios N. Troganis
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
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22
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Takis PG, Papavasileiou KD, Peristeras LD, Melissas VS, Troganis AN. Probing micro-solvation in “numbers”: the case of neutral dipeptides in water. Phys Chem Chem Phys 2013; 15:7354-62. [DOI: 10.1039/c3cp44606a] [Citation(s) in RCA: 8] [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: 11/21/2022]
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23
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Takis PG, Melissas VS, Troganis AN. A “hidden” role of amino and imino groups is unveiled during the micro-solvation study of three biomolecule groups in water. NEW J CHEM 2012. [DOI: 10.1039/c2nj40390k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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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