1
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Ansone L, Rovite V, Brīvība M, Jagare L, Pelcmane L, Borisova D, Thews A, Leiminger R, Kloviņš J. Longitudinal NMR-Based Metabolomics Study Reveals How Hospitalized COVID-19 Patients Recover: Evidence of Dyslipidemia and Energy Metabolism Dysregulation. Int J Mol Sci 2024; 25:1523. [PMID: 38338803 PMCID: PMC10855192 DOI: 10.3390/ijms25031523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Long COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), can manifest as long-term symptoms in multiple organ systems, including respiratory, cardiovascular, neurological, and metabolic systems. In patients with severe COVID-19, immune dysregulation is significant, and the relationship between metabolic regulation and immune response is of great interest in determining the pathophysiological mechanisms. We aimed to characterize the metabolomic footprint of recovering severe COVID-19 patients at three consecutive timepoints and compare metabolite levels to controls. Our findings add proof of dysregulated amino acid metabolism in the acute phase and dyslipidemia, glycoprotein level alterations, and energy metabolism disturbances in severe COVID-19 patients 3-4 months post-hospitalization.
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Affiliation(s)
- Laura Ansone
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
| | - Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
| | - Lauma Jagare
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
| | - Līva Pelcmane
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
| | - Daniella Borisova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
| | - Anne Thews
- Bruker BioSpin GmbH & Co., Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany; (A.T.); (R.L.)
| | - Roland Leiminger
- Bruker BioSpin GmbH & Co., Rudolf-Plank-Straße 23, 76275 Ettlingen, Germany; (A.T.); (R.L.)
| | - Jānis Kloviņš
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (M.B.); (L.J.); (L.P.); (D.B.)
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2
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Ricci A, Dugo M, Pisanu ME, De Cecco L, Raspagliesi F, Valeri B, Veneroni S, Chirico M, Palombelli G, Daidone MG, Podo F, Canese R, Mezzanzanica D, Bagnoli M, Iorio E. Impact of Cold Ischemia on the Stability of 1H-MRS-Detected Metabolic Profiles of Ovarian Cancer Specimens. J Proteome Res 2024; 23:483-493. [PMID: 38109371 DOI: 10.1021/acs.jproteome.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Proton magnetic resonance spectroscopy (1H-MRS) of surgically collected tumor specimens may contribute to investigating cancer metabolism and the significance of the "total choline" (tCho) peak (3.2 ppm) as malignancy and therapy response biomarker. To ensure preservation of intrinsic metabolomic information, standardized handling procedures are needed. The effects of time to freeze (cold ischemia) were evaluated in (a) surgical epithelial ovarian cancer (EOC) specimens using high-resolution (HR) 1H-MRS (9.4 T) of aqueous extracts and (b) preclinical EOC samples (xenografts in SCID mice) investigated by in vivo MRI-guided 1H-MRS (4.7 T) and by HR-1H-MRS (9.4 T) of tumor extracts or intact fragments (using magic-angle-spinning (MAS) technology). No significant changes were found in the levels of 27 of 29 MRS-detected metabolites (including the tCho profile) in clinical specimens up to 2 h cold ischemia, besides an increase in lysine and a decrease in glutathione. EOC xenografts showed a 2-fold increase in free choline within 2 h cold ischemia, without further significant changes for any MRS-detected metabolite (including phosphocholine and tCho) up to 6 h. At shorter times (≤1 h), HR-MAS analyses showed unaltered tCho components, along with significant changes in lactate, glutamate, and glutamine. Our results support the view that a time to freeze of 1 h represents a safe threshold to ensure the maintenance of a reliable tCho profile in EOC specimens.
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Affiliation(s)
- Alessandro Ricci
- Notified Body 0373 Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Matteo Dugo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Maria Elena Pisanu
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Loris De Cecco
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Francesco Raspagliesi
- Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Barbara Valeri
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Silvia Veneroni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Mattea Chirico
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Gianmauro Palombelli
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Maria Grazia Daidone
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Franca Podo
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Rossella Canese
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Delia Mezzanzanica
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Marina Bagnoli
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Egidio Iorio
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
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3
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Di Cesare F, Calgaro M, Ghini V, Squarzanti DF, De Prisco A, Visciglia A, Zanetta P, Rolla R, Savoia P, Amoruso A, Azzimonti B, Vitulo N, Tenori L, Luchinat C, Pane M. Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals. J Proteome Res 2023; 22:3866-3878. [PMID: 37970754 PMCID: PMC10696601 DOI: 10.1021/acs.jproteome.3c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 11/17/2023]
Abstract
Probiotics are live microorganisms that confer health benefits when administered in adequate amounts. They are used to promote gut health and alleviate various disorders. Recently, there has been an increasing interest in the potential effects of probiotics on human physiology. In the presented study, the effects of probiotic treatment on the metabolic profiles of human urine and serum using a nuclear magnetic resonance (NMR)-based metabonomic approach were investigated. Twenty-one healthy volunteers were enrolled in the study, and they received two different dosages of probiotics for 8 weeks. During the study, urine and serum samples were collected from volunteers before and during probiotic supplementation. The results showed that probiotics had a significant impact on the urinary and serum metabolic profiles without altering their phenotypes. This study demonstrated the effects of probiotics in terms of variations of metabolite levels resulting also from the different probiotic posology. Overall, the results suggest that probiotic administration may affect both urine and serum metabolomes, although more research is needed to understand the mechanisms and clinical implications of these effects. NMR-based metabonomic analysis of biofluids is a powerful tool for monitoring host-gut microflora dynamic interaction as well as for assessing the individual response to probiotic treatment.
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Affiliation(s)
- Francesca Di Cesare
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Matteo Calgaro
- Department
of Biotechnology, University of Verona, Strada le Grazie, 15, Verona 37134, Italy
| | - Veronica Ghini
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Diletta Francesca Squarzanti
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
- Center
for Translational Research on Autoimmune and Allergic Diseases (CAAD),
Department of Health Sciences (DiSS), University
of Piemonte Orientale (UPO), Corso Trieste, 15, Novara 28100, Italy
| | | | | | - Paola Zanetta
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
- Center
for Translational Research on Autoimmune and Allergic Diseases (CAAD),
Department of Health Sciences (DiSS), University
of Piemonte Orientale (UPO), Corso Trieste, 15, Novara 28100, Italy
| | - Roberta Rolla
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
| | - Paola Savoia
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
| | - Angela Amoruso
- Probiotical
Research Srl, Via Enrico
Mattei, 3, Novara 28100, Italy
| | - Barbara Azzimonti
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
- Center
for Translational Research on Autoimmune and Allergic Diseases (CAAD),
Department of Health Sciences (DiSS), University
of Piemonte Orientale (UPO), Corso Trieste, 15, Novara 28100, Italy
| | - Nicola Vitulo
- Department
of Biotechnology, University of Verona, Strada le Grazie, 15, Verona 37134, Italy
| | - Leonardo Tenori
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
| | - Claudio Luchinat
- Consorzio
Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Giotto
Biotech S.r.l., Via Madonna
del Piano, 6, Sesto Fiorentino, Firenze 50019, Italy
| | - Marco Pane
- Probiotical
Research Srl, Via Enrico
Mattei, 3, Novara 28100, Italy
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4
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Ghini V, Meoni G, Vignoli A, Di Cesare F, Tenori L, Turano P, Luchinat C. Fingerprinting and profiling in metabolomics of biosamples. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 138-139:105-135. [PMID: 38065666 DOI: 10.1016/j.pnmrs.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 12/18/2023]
Abstract
This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.
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Affiliation(s)
- Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy; Giotto Biotech S.r.l., Sesto Fiorentino, Italy.
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5
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Ghini V, Vieri W, Celli T, Pecchioli V, Boccia N, Alonso-Vásquez T, Pelagatti L, Fondi M, Luchinat C, Bertini L, Vannucchi V, Landini G, Turano P. COVID-19: A complex disease with a unique metabolic signature. PLoS Pathog 2023; 19:e1011787. [PMID: 37943960 PMCID: PMC10662774 DOI: 10.1371/journal.ppat.1011787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/21/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Plasma of COVID-19 patients contains a strong metabolomic/lipoproteomic signature, revealed by the NMR analysis of a cohort of >500 patients sampled during various waves of COVID-19 infection, corresponding to the spread of different variants, and having different vaccination status. This composite signature highlights common traits of the SARS-CoV-2 infection. The most dysregulated molecules display concentration trends that scale with disease severity and might serve as prognostic markers for fatal events. Metabolomics evidence is then used as input data for a sex-specific multi-organ metabolic model. This reconstruction provides a comprehensive view of the impact of COVID-19 on the entire human metabolism. The human (male and female) metabolic network is strongly impacted by the disease to an extent dictated by its severity. A marked metabolic reprogramming at the level of many organs indicates an increase in the generic energetic demand of the organism following infection. Sex-specific modulation of immune response is also suggested.
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Affiliation(s)
- Veronica Ghini
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Walter Vieri
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tommaso Celli
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Valentina Pecchioli
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Nunzia Boccia
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Tania Alonso-Vásquez
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Lorenzo Pelagatti
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino Florence, Italy
| | - Laura Bertini
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Vieri Vannucchi
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Giancarlo Landini
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Paola Turano
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino Florence, Italy
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Alcicek S, Put P, Kubrak A, Alcicek FC, Barskiy D, Gloeggler S, Dybas J, Pustelny S. Zero- to low-field relaxometry of chemical and biological fluids. Commun Chem 2023; 6:165. [PMID: 37542142 PMCID: PMC10403525 DOI: 10.1038/s42004-023-00965-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Nuclear magnetic resonance (NMR) relaxometry is an analytical method that provides information about molecular environments, even for NMR "silent" molecules (spin-0), by analyzing the properties of NMR signals versus the magnitude of the longitudinal field. Conventionally, this technique is performed at fields much higher than Earth's magnetic field, but our work focuses on NMR relaxometry at zero and ultra-low magnetic fields (ZULFs). Operating under such conditions allows us to investigate slow (bio)chemical processes occurring on a timescale from milliseconds to seconds, which coincide with spin evolution. ZULFs also minimize T2 line broadening in heterogeneous samples resulting from magnetic susceptibility. Here, we use ZULF NMR relaxometry to analyze (bio)chemical compounds containing 1H-13C, 1H-15N, and 1H-31P spin pairs. We also detected high-quality ULF NMR spectra of human whole-blood at 0.8 μT, despite a shortening of spin relaxation by blood proteomes (e.g., hemoglobin). Information on proton relaxation times of blood, a potential early biomarker of inflammation, can be acquired in under a minute using inexpensive, portable/small-size NMR spectrometers based on atomic magnetometers.
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Affiliation(s)
- Seyma Alcicek
- Goethe University Frankfurt, University Hospital, Institute of Neuroradiology, 60528, Frankfurt am Main, Germany.
- Institute of Physics Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University in Kraków, 30-348, Kraków, Poland.
| | - Piotr Put
- Institute of Physics Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University in Kraków, 30-348, Kraków, Poland
| | - Adam Kubrak
- Faculty of Chemistry, Jagiellonian University in Kraków, 30-387, Krakow, Poland
| | - Fatih Celal Alcicek
- Jagiellonian Center for Experimental Therapeutics, Jagiellonian University in Kraków, 30-348, Kraków, Poland
| | - Danila Barskiy
- Helmholtz Institute Mainz, GSI Helmholtz Center for Heavy Ion Research GmbH, 55128, Mainz, Germany
- Institute of Physics, Johannes Gutenberg-Universität, 55128, Mainz, Germany
| | - Stefan Gloeggler
- Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Jakub Dybas
- Jagiellonian Center for Experimental Therapeutics, Jagiellonian University in Kraków, 30-348, Kraków, Poland
| | - Szymon Pustelny
- Institute of Physics Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University in Kraków, 30-348, Kraków, Poland.
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7
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Madrid-Gambin F, Oller S, Marco S, Pozo ÓJ, Andres-Lacueva C, Llorach R. Quantitative plasma profiling by 1H NMR-based metabolomics: impact of sample treatment. Front Mol Biosci 2023; 10:1125582. [PMID: 37333016 PMCID: PMC10273206 DOI: 10.3389/fmolb.2023.1125582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction: There is evidence that sample treatment of blood-based biosamples may affect integral signals in nuclear magnetic resonance-based metabolomics. The presence of macromolecules in plasma/serum samples makes investigating low-molecular-weight metabolites challenging. It is particularly relevant in the targeted approach, in which absolute concentrations of selected metabolites are often quantified based on the area of integral signals. Since there are a few treatments of plasma/serum samples for quantitative analysis without a universally accepted method, this topic remains of interest for future research. Methods: In this work, targeted metabolomic profiling of 43 metabolites was performed on pooled plasma to compare four methodologies consisting of Carr-Purcell-Meiboom-Gill (CPMG) editing, ultrafiltration, protein precipitation with methanol, and glycerophospholipid solid-phase extraction (g-SPE) for phospholipid removal; prior to NMR metabolomics analysis. The effect of the sample treatments on the metabolite concentrations was evaluated using a permutation test of multiclass and pairwise Fisher scores. Results: Results showed that methanol precipitation and ultrafiltration had a higher number of metabolites with coefficient of variation (CV) values above 20%. G-SPE and CPMG editing demonstrated better precision for most of the metabolites analyzed. However, differential quantification performance between procedures were metabolite-dependent. For example, pairwise comparisons showed that methanol precipitation and CPMG editing were suitable for quantifying citrate, while g-SPE showed better results for 2-hydroxybutyrate and tryptophan. Discussion: There are alterations in the absolute concentration of various metabolites that are dependent on the procedure. Considering these alterations is essential before proceeding with the quantification of treatment-sensitive metabolites in biological samples for improving biomarker discovery and biological interpretations. The study demonstrated that g-SPE and CPMG editing are effective methods for removing proteins and phospholipids from plasma samples for quantitative NMR analysis of metabolites. However, careful consideration should be given to the specific metabolites of interest and their susceptibility to the sample treatment procedures. These findings contribute to the development of optimized sample preparation protocols for metabolomics studies using NMR spectroscopy.
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Affiliation(s)
- Francisco Madrid-Gambin
- Applied Metabolomics Research Group, IMIM—Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sergio Oller
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Barcelona, Spain
| | - Santiago Marco
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Barcelona, Spain
| | - Óscar J. Pozo
- Applied Metabolomics Research Group, IMIM—Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Sant Coloma de Gramanet, Spain
- Food Innovation Network (XIA), Santa Coloma de Gramanet, Spain
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB), Santa Coloma de Gramanet, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Llorach
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Sant Coloma de Gramanet, Spain
- Food Innovation Network (XIA), Santa Coloma de Gramanet, Spain
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB), Santa Coloma de Gramanet, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
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8
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Wishart DS, Rout M, Lee BL, Berjanskii M, LeVatte M, Lipfert M. Practical Aspects of NMR-Based Metabolomics. Handb Exp Pharmacol 2023; 277:1-41. [PMID: 36271165 DOI: 10.1007/164_2022_613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for >40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada.
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcia LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Matthias Lipfert
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Reference Standard Management & NMR QC, Lonza Group AG, Visp, Switzerland
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9
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Bizkarguenaga M, Gil-Redondo R, Bruzzone C, Bernardo-Seisdedos G, Laín A, González-Valle B, Embade N, Mato JM, Millet O. Prospective Metabolomic Studies in Precision Medicine: The AKRIBEA Project. Handb Exp Pharmacol 2023; 277:275-297. [PMID: 36253553 DOI: 10.1007/164_2022_610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
For a long time, conventional medicine has analysed biomolecules to diagnose diseases. Yet, this approach has proven valid only for a limited number of metabolites and often through a bijective relationship with the disease (i.e. glucose relationship with diabetes), ultimately offering incomplete diagnostic value. Nowadays, precision medicine emerges as an option to improve the prevention and/or treatment of numerous pathologies, focusing on the molecular mechanisms, acting in a patient-specific dimension, and leveraging multiple contributing factors such as genetic, environmental, or lifestyle. Metabolomics grasps the required subcellular complexity while being sensitive to all these factors, which results in a most suitable technique for precision medicine. The aim of this chapter is to describe how NMR-based metabolomics can be integrated in the design of a precision medicine strategy, using the Precision Medicine Initiative of the Basque Country (the AKRIBEA project) as a case study. To that end, we will illustrate the procedures to be followed when conducting an NMR-based metabolomics study with a large cohort of individuals, emphasizing the critical points. The chapter will conclude with the discussion of some relevant biomedical applications.
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Affiliation(s)
- Maider Bizkarguenaga
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Rubén Gil-Redondo
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Chiara Bruzzone
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Ganeko Bernardo-Seisdedos
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Ana Laín
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Beatriz González-Valle
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Nieves Embade
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - José M Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Derio, Bizkaia, Spain.
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10
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Vignoli A, Meoni G, Ghini V, Di Cesare F, Tenori L, Luchinat C, Turano P. NMR-Based Metabolomics to Evaluate Individual Response to Treatments. Handb Exp Pharmacol 2023; 277:209-245. [PMID: 36318327 DOI: 10.1007/164_2022_618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of this chapter is to highlight the various aspects of metabolomics in relation to health and diseases, starting from the definition of metabolic space and of how individuals tend to maintain their own position in this space. Physio-pathological stimuli may cause individuals to lose their position and then regain it, or move irreversibly to other positions. By way of examples, mostly selected from our own work using 1H NMR on biological fluids, we describe the effects on the individual metabolomic fingerprint of mild external interventions, such as diet or probiotic administration. Then we move to pathologies (such as celiac disease, various types of cancer, viral infections, and other diseases), each characterized by a well-defined metabolomic fingerprint. We describe the effects of drugs on the disease fingerprint and on its reversal to a healthy metabolomic status. Drug toxicity can be also monitored by metabolomics. We also show how the individual metabolomic fingerprint at the onset of a disease may discriminate responders from non-responders to a given drug, or how it may be prognostic of e.g., cancer recurrence after many years. In parallel with fingerprinting, profiling (i.e., the identification and quantification of many metabolites and, in the case of selected biofluids, of the lipoprotein components that contribute to the 1H NMR spectral features) can provide hints on the metabolic pathways that are altered by a disease and assess their restoration after treatment.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy.
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11
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Benevelli F, Vella S, Crosta C, Demetrio E, Fischer C, Pupo M, Baila S. NMR as powerful technology for non-invasively monitoring cell health and expansion during bioprocessing. Biotechnol Bioeng 2022; 119:3497-3508. [PMID: 36000349 DOI: 10.1002/bit.28207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 11/11/2022]
Abstract
Over the last decades, the success of advanced cell therapies and the increasing production volumes of vaccines, proteins or viral vectors have raised the need of robust cell-based manufacturing processes for ensuring product quality and satisfying GMP requirements. The cultivation process of cells needs to be highly controlled for improved productivity, reduced variability and optimized bioprocesses. Cell cultures can be easily monitored using different technologies, which could deliver direct or indirect assessment of the cells' viability. Among these techniques, Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technology which permits the evaluation and the identification of key endogenous metabolites. NMR can provide information on the cell metabolic pathways, on the bioprocesses and is also capable to quickly test for impurities. In this study, NMR was successfully used as a technology for monitoring cell viability and expansion in different supports for cell growth (including bioreactors), in order to predict the bioprocess output and for the early identification of key metabolites linked to cell starvation. This investigation will allow the timely control of culture conditions and favour the optimization of the bioprocesses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Serena Vella
- Development Lead, Innovation and Development Department, Anemocyte S.r.l., Gerenzano, Italy
| | | | - Elena Demetrio
- Magnetic Resonance Spectroscopy Division, BioSpin Business Unit, Bruker Italia S.r.l., Milan, Italy
| | - Christian Fischer
- Pharmaceutical Business Unit, Bruker BioSpin GmbH, Ettlingen, Germany
| | - Marco Pupo
- Development Lead, Innovation and Development Department, Anemocyte S.r.l., Gerenzano, Italy
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12
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Meoni G, Tenori L, Schade S, Licari C, Pirazzini C, Bacalini MG, Garagnani P, Turano P, Trenkwalder C, Franceschi C, Mollenhauer B, Luchinat C. Metabolite and lipoprotein profiles reveal sex-related oxidative stress imbalance in de novo drug-naive Parkinson's disease patients. NPJ Parkinsons Dis 2022; 8:14. [PMID: 35136088 PMCID: PMC8826921 DOI: 10.1038/s41531-021-00274-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson’s disease (PD) is the neurological disorder showing the greatest rise in prevalence from 1990 to 2016. Despite clinical definition criteria and a tremendous effort to develop objective biomarkers, precise diagnosis of PD is still unavailable at early stage. In recent years, an increasing number of studies have used omic methods to unveil the molecular basis of PD, providing a detailed characterization of potentially pathological alterations in various biological specimens. Metabolomics could provide useful insights to deepen our knowledge of PD aetiopathogenesis, to identify signatures that distinguish groups of patients and uncover responsive biomarkers of PD that may be significant in early detection and in tracking the disease progression and drug treatment efficacy. The present work is the first large metabolomic study based on nuclear magnetic resonance (NMR) with an independent validation cohort aiming at the serum characterization of de novo drug-naive PD patients. Here, NMR is applied to sera from large training and independent validation cohorts of German subjects. Multivariate and univariate approaches are used to infer metabolic differences that characterize the metabolite and the lipoprotein profiles of newly diagnosed de novo drug-naive PD patients also in relation to the biological sex of the subjects in the study, evidencing a more pronounced fingerprint of the pathology in male patients. The presence of a validation cohort allowed us to confirm altered levels of acetone and cholesterol in male PD patients. By comparing the metabolites and lipoproteins levels among de novo drug-naive PD patients, age- and sex-matched healthy controls, and a group of advanced PD patients, we detected several descriptors of stronger oxidative stress.
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Affiliation(s)
- Gaia Meoni
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino, Florence, Italy
| | - Sebastian Schade
- Department of Clinical Neurophysiology, University Medical Center Goettingen, Goettingen, Germany
| | - Cristina Licari
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino, Florence, Italy
| | | | - Claudia Trenkwalder
- University Medical Center Goettingen, Department of Neurology and Paracelsus-Elena-Klinik, Kassel, Germany
| | - Claudio Franceschi
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy. .,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia.
| | - Brit Mollenhauer
- University Medical Center Goettingen, Department of Neurology and Paracelsus-Elena-Klinik, Kassel, Germany.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino, Florence, Italy.
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13
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Ghini V, Abuja PM, Polasek O, Kozera L, Laiho P, Anton G, Zins M, Klovins J, Metspalu A, Wichmann HE, Gieger C, Luchinat C, Zatloukal K, Turano P. Impact of the pre-examination phase on multicenter metabolomic studies. N Biotechnol 2022; 68:37-47. [PMID: 35066155 DOI: 10.1016/j.nbt.2022.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/23/2023]
Abstract
The development of metabolomics in clinical applications has been limited by the lack of validation in large multicenter studies. Large population cohorts and their biobanks are a valuable resource for acquiring insights into molecular disease mechanisms. Nevertheless, most of their collections are not tailored for metabolomics and have been created without specific attention to the pre-analytical requirements for high-quality metabolome assessment. Thus, comparing samples obtained by different pre-analytical procedures remains a major challenge. Here, 1H NMR-based analyses are used to demonstrate how human serum and plasma samples collected with different operating procedures within several large European cohort studies from the Biobanking and Biomolecular Resources Infrastructure - Large Prospective Cohorts (BBMRI-LPC) consortium can be easily revealed by supervised multivariate statistical analyses at the initial stages of the process, to avoid biases in the downstream analysis. The inter-biobank differences are discussed in terms of deviations from the validated CEN/TS 16945:2016 / ISO 23118:2021 norms. It clearly emerges that biobanks must adhere to the evidence-based guidelines in order to support wider-scale application of metabolomics in biomedicine, and that NMR spectroscopy is informative in comparing the quality of different sample sources in multi cohort/center studies.
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Affiliation(s)
- Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy; Center of Magnetic Resonance (CERM), University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy; Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy
| | - Peter M Abuja
- Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010, Graz, Austria
| | - Ozren Polasek
- Department for Large Population Studies, University of Split, Šoltanska 2, HR-21000, Split, Croatia; Gen-info Ltd, Ružmarinka ul. 17, 10000, Zagreb, Croatia
| | - Lukasz Kozera
- BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
| | - Päivi Laiho
- Institute for Molecular Medicine Finland, National Institute for Health and Welfare, THL, University of Helsinki, 00290, Helsinki, Finland
| | - Gabriele Anton
- Molecular Epidemiology, Helmholtz-Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Marie Zins
- Population-based Epidemiological Cohorts Unit-UMS 11, Inserm, 16 Avenue Paul Vaillant Couturier, 94800, Villejuif, France
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Rātsupītes iela 1, Kurzemes rajons, Rīga, LV-1067, Latvia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - H-Erich Wichmann
- Institute of Epidemiology, Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy; Center of Magnetic Resonance (CERM), University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy; Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy
| | - Kurt Zatloukal
- Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010, Graz, Austria.
| | - Paola Turano
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy; Center of Magnetic Resonance (CERM), University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy; Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.
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14
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OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6585976. [DOI: 10.1093/femsre/fuac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
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15
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Gómez-Cebrián N, Vázquez Ferreiro P, Carrera Hueso FJ, Poveda Andrés JL, Puchades-Carrasco L, Pineda-Lucena A. Pharmacometabolomics by NMR in Oncology: A Systematic Review. Pharmaceuticals (Basel) 2021; 14:ph14101015. [PMID: 34681239 PMCID: PMC8539252 DOI: 10.3390/ph14101015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacometabolomics (PMx) studies aim to predict individual differences in treatment response and in the development of adverse effects associated with specific drug treatments. Overall, these studies inform us about how individuals will respond to a drug treatment based on their metabolic profiles obtained before, during, or after the therapeutic intervention. In the era of precision medicine, metabolic profiles hold great potential to guide patient selection and stratification in clinical trials, with a focus on improving drug efficacy and safety. Metabolomics is closely related to the phenotype as alterations in metabolism reflect changes in the preceding cascade of genomics, transcriptomics, and proteomics changes, thus providing a significant advance over other omics approaches. Nuclear Magnetic Resonance (NMR) is one of the most widely used analytical platforms in metabolomics studies. In fact, since the introduction of PMx studies in 2006, the number of NMR-based PMx studies has been continuously growing and has provided novel insights into the specific metabolic changes associated with different mechanisms of action and/or toxic effects. This review presents an up-to-date summary of NMR-based PMx studies performed over the last 10 years. Our main objective is to discuss the experimental approaches used for the characterization of the metabolic changes associated with specific therapeutic interventions, the most relevant results obtained so far, and some of the remaining challenges in this area.
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Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
| | | | | | | | - Leonor Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
- Correspondence: (L.P.-C.); (A.P.-L.); Tel.: +34-963246713 (L.P.-C.)
| | - Antonio Pineda-Lucena
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, 31008 Navarra, Spain
- Correspondence: (L.P.-C.); (A.P.-L.); Tel.: +34-963246713 (L.P.-C.)
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16
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Lee S, Ku JY, Kang BJ, Kim KH, Ha HK, Kim S. A Unique Urinary Metabolic Feature for the Determination of Bladder Cancer, Prostate Cancer, and Renal Cell Carcinoma. Metabolites 2021; 11:metabo11090591. [PMID: 34564407 PMCID: PMC8468099 DOI: 10.3390/metabo11090591] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 01/16/2023] Open
Abstract
Prostate cancer (PCa), bladder cancer (BCa), and renal cell carcinoma (RCC) are the most prevalent cancer among urological cancers. However, there are no cancer-specific symptoms that can differentiate them as well as early clinical signs of urological malignancy. Furthermore, many metabolic studies have been conducted to discover their biomarkers, but the metabolic profiling study to discriminate between these cancers have not yet been described. Therefore, in this study, we aimed to investigate the urinary metabolic differences in male patients with PCa (n = 24), BCa (n = 29), and RCC (n = 12) to find the prominent combination of metabolites between cancers. Based on 1H NMR analysis, orthogonal partial least-squares discriminant analysis was applied to find distinct metabolites among cancers. Moreover, the ranked analysis of covariance by adjusting a potential confounding as age revealed that 4-hydroxybenzoate, N-methylhydantoin, creatinine, glutamine, and acetate had significantly different metabolite levels among groups. The receiver operating characteristic analysis created by prominent five metabolites showed the great discriminatory accuracy with area under the curve (AUC) > 0.7 for BCa vs. RCC, PCa vs. BCa, and RCC vs. PCa. This preliminary study compares the metabolic profiles of BCa, PCa, and RCC, and reinforces the exploratory role of metabolomics in the investigation of human urine.
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Affiliation(s)
- Sujin Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Institute for Plastic Information and Energy Materials, Pusan National University, Busandaehak-ro 63, Geumjeong-gu, Busan 46241, Korea;
| | - Ja Yoon Ku
- Department of Urology, Dongnam Institute of Radiological & Medical Sciences Cancer Center, Busan 46033, Korea;
| | - Byeong Jin Kang
- Department of Urology, College of Medicine, Pusan National University, Busan 49241, Korea; (B.J.K.); (K.H.K.)
| | - Kyung Hwan Kim
- Department of Urology, College of Medicine, Pusan National University, Busan 49241, Korea; (B.J.K.); (K.H.K.)
| | - Hong Koo Ha
- Department of Urology, College of Medicine, Pusan National University and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Korea;
| | - Suhkmann Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Institute for Plastic Information and Energy Materials, Pusan National University, Busandaehak-ro 63, Geumjeong-gu, Busan 46241, Korea;
- Correspondence: ; Tel.: +82-51-510-2240
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17
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Detection of Lung Cancer via Blood Plasma and 1H-NMR Metabolomics: Validation by a Semi-Targeted and Quantitative Approach Using a Protein-Binding Competitor. Metabolites 2021; 11:metabo11080537. [PMID: 34436478 PMCID: PMC8401204 DOI: 10.3390/metabo11080537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 01/03/2023] Open
Abstract
Metabolite profiling of blood plasma, by proton nuclear magnetic resonance (1H-NMR) spectroscopy, offers great potential for early cancer diagnosis and unraveling disruptions in cancer metabolism. Despite the essential attempts to standardize pre-analytical and external conditions, such as pH or temperature, the donor-intrinsic plasma protein concentration is highly overlooked. However, this is of utmost importance, since several metabolites bind to these proteins, resulting in an underestimation of signal intensities. This paper describes a novel 1H-NMR approach to avoid metabolite binding by adding 4 mM trimethylsilyl-2,2,3,3-tetradeuteropropionic acid (TSP) as a strong binding competitor. In addition, it is demonstrated, for the first time, that maleic acid is a reliable internal standard to quantify the human plasma metabolites without the need for protein precipitation. Metabolite spiking is further used to identify the peaks of 62 plasma metabolites and to divide the 1H-NMR spectrum into 237 well-defined integration regions, representing these 62 metabolites. A supervised multivariate classification model, trained using the intensities of these integration regions (areas under the peaks), was able to differentiate between lung cancer patients and healthy controls in a large patient cohort (n = 160), with a specificity, sensitivity, and area under the curve of 93%, 85%, and 0.95, respectively. The robustness of the classification model is shown by validation in an independent patient cohort (n = 72).
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18
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Ghini V, Abuja PM, Polasek O, Kozera L, Laiho P, Anton G, Zins M, Klovins J, Metspalu A, Wichmann HE, Gieger C, Luchinat C, Zatloukal K, Turano P. Metabolomic Fingerprints in Large Population Cohorts: Impact of Preanalytical Heterogeneity. Clin Chem 2021; 67:1153-1155. [PMID: 34223627 DOI: 10.1093/clinchem/hvab092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino (FI), Italy
| | - Peter M Abuja
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ozren Polasek
- Department for Large Population Studies, University of Split, Split, Croatia.,Gen-Info Ltd, Zagreb, Croatia
| | | | - Päivi Laiho
- Institute for Molecular Medicine Finland, & National Institute for Health and Welfare, THL, University of Helsinki, Helsinki, Finland
| | - Gabriele Anton
- Molecular Epidemiology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Marie Zins
- Population-based Epidemiological Cohorts Unit-UMS 11, Inserm, Villejuif, France
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Rīga, Latvia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - H-Erich Wichmann
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino (FI), Italy.,Center of Magnetic Resonance (CERM), University of Florence, Sesto Fiorentino (FI), Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
| | - Kurt Zatloukal
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Paola Turano
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino (FI), Italy.,Center of Magnetic Resonance (CERM), University of Florence, Sesto Fiorentino (FI), Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
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Bendinelli B, Vignoli A, Palli D, Assedi M, Ambrogetti D, Luchinat C, Caini S, Saieva C, Turano P, Masala G. Prediagnostic circulating metabolites in female breast cancer cases with low and high mammographic breast density. Sci Rep 2021; 11:13025. [PMID: 34158597 PMCID: PMC8219761 DOI: 10.1038/s41598-021-92508-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/11/2021] [Indexed: 02/05/2023] Open
Abstract
Mammographic breast density (MBD) is a strong independent risk factor for breast cancer (BC). We designed a matched case-case study in the EPIC Florence cohort, to evaluate possible associations between the pre-diagnostic metabolomic profile and the risk of BC in high- versus low-MBD women who developed BC during the follow-up. A case-case design with 100 low-MBD (MBD ≤ 25%) and 100 high-MDB BC cases (MBD > 50%) was performed. Matching variables included age, year and type of mammographic examination. 1H NMR metabolomic spectra were available for 87 complete case-case sets. The conditional logistic analyses showed an inverse association between serum levels of alanine, leucine, tyrosine, valine, lactic acid, pyruvic acid, triglycerides lipid main fraction and 11 VLDL lipid subfractions and high-MBD cases. Acetic acid was directly associated with high-MBD cases. In models adjusted for confounding variables, tyrosine remained inversely associated with high-MBD cases while 3 VLDL subfractions of free cholesterol emerged as directly associated with high-MBD cases. A pathway analysis showed that the "phenylalanine, tyrosine and tryptophan pathway" emerged and persisted after applying the FDR procedure. The supervised OPLS-DA analysis revealed a slight but significant separation between high- and low-MBD cases. This case-case study suggested a possible role for pre-diagnostic levels of tyrosine in modulating the risk of BC in high- versus low-MBD women. Moreover, some differences emerged in the pre-diagnostic concentration of other metabolites as well in the metabolomic fingerprints among the two groups of patients.
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Affiliation(s)
- Benedetta Bendinelli
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
| | - Alessia Vignoli
- grid.20765.360000 0004 7402 7708Consorzio Interuniversitario Risonanze Magnetiche Di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy
| | - Domenico Palli
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
| | - Melania Assedi
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
| | - Daniela Ambrogetti
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
| | - Claudio Luchinat
- grid.8404.80000 0004 1757 2304Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy ,grid.8404.80000 0004 1757 2304Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Saverio Caini
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
| | - Calogero Saieva
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
| | - Paola Turano
- grid.8404.80000 0004 1757 2304Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy ,grid.8404.80000 0004 1757 2304Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Giovanna Masala
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Cosimo il Vecchio 2, 50139 Florence, Italy
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20
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From bedside to bench-practical considerations to avoid pre-analytical pitfalls and assess sample quality for high-resolution metabolomics and lipidomics analyses of body fluids. Anal Bioanal Chem 2021; 413:5567-5585. [PMID: 34159398 PMCID: PMC8410705 DOI: 10.1007/s00216-021-03450-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/24/2021] [Accepted: 05/31/2021] [Indexed: 11/22/2022]
Abstract
The stability of lipids and other metabolites in human body fluids ranges from very stable over several days to very unstable within minutes after sample collection. Since the high-resolution analytics of metabolomics and lipidomics approaches comprise all these compounds, the handling of body fluid samples, and thus the pre-analytical phase, is of utmost importance to obtain valid profiling data. This phase consists of two parts, sample collection in the hospital (“bedside”) and sample processing in the laboratory (“bench”). For sample quality, the apparently simple steps in the hospital are much more critical than the “bench” side handling, where (bio)analytical chemists focus on highly standardized processing for high-resolution analysis under well-controlled conditions. This review discusses the most critical pre-analytical steps for sample quality from patient preparation; collection of body fluids (blood, urine, cerebrospinal fluid) to sample handling, transport, and storage in freezers; and subsequent thawing using current literature, as well as own investigations and practical experiences in the hospital. Furthermore, it provides guidance for (bio)analytical chemists to detect and prevent potential pre-analytical pitfalls at the “bedside,” and how to assess the quality of already collected body fluid samples. A knowledge base is provided allowing one to decide whether or not the sample quality is acceptable for its intended use in distinct profiling approaches and to select the most suitable samples for high-resolution metabolomics and lipidomics investigations.
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21
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Wang Z, Pisano S, Ghini V, Kadeřávek P, Zachrdla M, Pelupessy P, Kazmierczak M, Marquardsen T, Tyburn JM, Bouvignies G, Parigi G, Luchinat C, Ferrage F. Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR. J Am Chem Soc 2021; 143:9393-9404. [PMID: 34133154 DOI: 10.1021/jacs.1c01388] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, the systematic investigation of metabolites in biological fluids, cells, or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in a myriad of biological processes, as substrates and products of enzymatic reactions but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are still scarce to date. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite (or other small molecules)-protein interactions in biological fluids for interactomics or pharmaceutical applications.
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Affiliation(s)
- Ziqing Wang
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Simone Pisano
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Morgan Kazmierczak
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l'Industrie BP 10002, 67166 Cedex Wissembourg, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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22
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Vignoli A, Risi E, McCartney A, Migliaccio I, Moretti E, Malorni L, Luchinat C, Biganzoli L, Tenori L. Precision Oncology via NMR-Based Metabolomics: A Review on Breast Cancer. Int J Mol Sci 2021; 22:ijms22094687. [PMID: 33925233 PMCID: PMC8124948 DOI: 10.3390/ijms22094687] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Precision oncology is an emerging approach in cancer care. It aims at selecting the optimal therapy for the right patient by considering each patient’s unique disease and individual health status. In the last years, it has become evident that breast cancer is an extremely heterogeneous disease, and therefore, patients need to be appropriately stratified to maximize survival and quality of life. Gene-expression tools have already positively assisted clinical decision making by estimating the risk of recurrence and the potential benefit from adjuvant chemotherapy. However, these approaches need refinement to further reduce the proportion of patients potentially exposed to unnecessary chemotherapy. Nuclear magnetic resonance (NMR) metabolomics has demonstrated to be an optimal approach for cancer research and has provided significant results in BC, in particular for prognostic and stratification purposes. In this review, we give an update on the status of NMR-based metabolomic studies for the biochemical characterization and stratification of breast cancer patients using different biospecimens (breast tissue, blood serum/plasma, and urine).
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Emanuela Risi
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Amelia McCartney
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
- School of Clinical Sciences, Monash University, Melbourne 3800, Australia
| | - Ilenia Migliaccio
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Erica Moretti
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Luca Malorni
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), 50019 Sesto Fiorentino, Italy
- Correspondence: ; Tel.: +39-055-457-4296
| | - Laura Biganzoli
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), 50019 Sesto Fiorentino, Italy
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23
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Metabolomic/lipidomic profiling of COVID-19 and individual response to tocilizumab. PLoS Pathog 2021; 17:e1009243. [PMID: 33524041 PMCID: PMC7877736 DOI: 10.1371/journal.ppat.1009243] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/11/2021] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
The current pandemic emergence of novel coronavirus disease (COVID-19) poses a relevant threat to global health. SARS-CoV-2 infection is characterized by a wide range of clinical manifestations, ranging from absence of symptoms to severe forms that need intensive care treatment. Here, plasma-EDTA samples of 30 patients compared with age- and sex-matched controls were analyzed via untargeted nuclear magnetic resonance (NMR)-based metabolomics and lipidomics. With the same approach, the effect of tocilizumab administration was evaluated in a subset of patients. Despite the heterogeneity of the clinical symptoms, COVID-19 patients are characterized by common plasma metabolomic and lipidomic signatures (91.7% and 87.5% accuracy, respectively, when compared to controls). Tocilizumab treatment resulted in at least partial reversion of the metabolic alterations due to SARS-CoV-2 infection. In conclusion, NMR-based metabolomic and lipidomic profiling provides novel insights into the pathophysiological mechanism of human response to SARS-CoV-2 infection and to monitor treatment outcomes. The current COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is markedly affecting the world population. Here we report about the small-molecule profile of patients hospitalized during the first wave of the COVID-19 pandemic in Florence (Italy). Using magnetic resonance spectroscopy, we showed that the infection induces profound changes in the metabolome. The analysis of the specific metabolite changes and correlations with clinical data enabled the identification of potential biochemical determinants of the disease fingerprint. We also followed how metabolic alterations revert towards those of the control group upon treatment with tocilizumab, a recombinant humanized monoclonal antibody against the interleukin-6 receptor. These results open up possibilities for the monitoring of novel patients and their individual response to treatment.
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24
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Role of Sphingosine 1-Phosphate Signalling Axis in Muscle Atrophy Induced by TNFα in C2C12 Myotubes. Int J Mol Sci 2021; 22:ijms22031280. [PMID: 33525436 PMCID: PMC7866171 DOI: 10.3390/ijms22031280] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle atrophy is characterized by a decrease in muscle mass causing reduced agility, increased fatigability and higher risk of bone fractures. Inflammatory cytokines, such as tumor necrosis factor-alpha (TNFα), are strong inducers of skeletal muscle atrophy. The bioactive sphingolipid sphingosine 1-phoshate (S1P) plays an important role in skeletal muscle biology. S1P, generated by the phosphorylation of sphingosine catalyzed by sphingosine kinase (SK1/2), exerts most of its actions through its specific receptors, S1P1-5. Here, we provide experimental evidence that TNFα induces atrophy and autophagy in skeletal muscle C2C12 myotubes, modulating the expression of specific markers and both active and passive membrane electrophysiological properties. NMR-metabolomics provided a clear picture of the deep remodelling of skeletal muscle fibre metabolism induced by TNFα challenge. The cytokine is responsible for the modulation of S1P signalling axis, upregulating mRNA levels of S1P2 and S1P3 and downregulating those of SK2. TNFα increases the phosphorylated form of SK1, readout of its activation. Interestingly, pharmacological inhibition of SK1 and specific antagonism of S1P3 prevented the increase in autophagy markers and the changes in the electrophysiological properties of C2C12 myotubes without affecting metabolic remodelling induced by the cytokine, highlighting the involvement of S1P signalling axis on TNFα-induced atrophy in skeletal muscle.
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Gómez-Cebrián N, Rojas-Benedicto A, Albors-Vaquer A, Bellosillo B, Besses C, Martínez-López J, Pineda-Lucena A, Puchades-Carrasco L. Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. Cancers (Basel) 2021; 13:cancers13030482. [PMID: 33513807 PMCID: PMC7865636 DOI: 10.3390/cancers13030482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Current diagnosis of myeloproliferative neoplasms (MPNs), including polycythemia vera (PV) and essential thrombocythemia (ET), is controversial due to limitations associated with the lack of reproducibility, subjectivity and the presence of common somatic mutations in the driver genes. Metabolomics represents a powerful approach to identify altered metabolites that can differentiate between disease status at the time of diagnosis. The objective of this study was to characterize the serum metabolic profile of MPNs patients (PV and ET) and compare it with healthy controls (HC) and secondary thrombocytosis (ST) patients. The analysis revealed metabolites following similar trends between PV and ET patients, as well as unique significant differences in the serum metabolite levels of MNPs patients compared to HC and ST patients. These results could contribute to better differentiate patients with these diseases from HC and ST patients. Abstract Most common myeloproliferative neoplasms (MPNs) include polycythemia vera (PV) and essential thrombocythemia (ET). Accurate diagnosis of these disorders remains a clinical challenge due to the lack of specific clinical or molecular features in some patients enabling their discrimination. Metabolomics has been shown to be a powerful tool for the discrimination between different hematological diseases through the analysis of patients’ serum metabolic profiles. In this pilot study, the potential of NMR-based metabolomics to characterize the serum metabolic profile of MPNs patients (PV, ET), as well as its comparison with the metabolic profile of healthy controls (HC) and secondary thrombocytosis (ST) patients, was assessed. The metabolic profile of PV and ET patients, compared with HC, exhibited higher levels of lysine and decreased levels of acetoacetic acid, glutamate, polyunsaturated fatty acids (PUFAs), scyllo-inositol and 3-hydroxyisobutyrate. Furthermore, ET patients, compared with HC and ST patients, were characterized by decreased levels of formate, N-acetyl signals from glycoproteins (NAC) and phenylalanine, while the serum profile of PV patients, compared with HC, showed increased concentrations of lactate, isoleucine, creatine and glucose, as well as lower levels of choline-containing metabolites. The overall analysis revealed significant metabolic alterations mainly associated with energy metabolism, the TCA cycle, along with amino acid and lipid metabolism. These results underscore the potential of metabolomics for identifying metabolic alterations in the serum of MPNs patients that could contribute to improving the clinical management of these diseases.
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Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (N.G.-C.); (A.R.-B.); (A.A.-V.); (A.P.-L.)
| | - Ayelén Rojas-Benedicto
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (N.G.-C.); (A.R.-B.); (A.A.-V.); (A.P.-L.)
| | - Arturo Albors-Vaquer
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (N.G.-C.); (A.R.-B.); (A.A.-V.); (A.P.-L.)
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar Medical Research Institute, 08003 Barcelona, Spain;
| | - Carlos Besses
- Department of Hematology, Hospital Del Mar Medical Research Institute, 08003 Barcelona, Spain;
| | - Joaquín Martínez-López
- Department of Hematology, Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (N.G.-C.); (A.R.-B.); (A.A.-V.); (A.P.-L.)
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, Universidad de Navarra, 28040 Pamplona, Spain
| | - Leonor Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (N.G.-C.); (A.R.-B.); (A.A.-V.); (A.P.-L.)
- Correspondence: ; Tel.: +34-96-124-6713
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Ghini V, Laera L, Fantechi B, del Monte F, Benelli M, McCartney A, Tenori L, Luchinat C, Pozzessere D. Metabolomics to Assess Response to Immune Checkpoint Inhibitors in Patients with Non-Small-Cell Lung Cancer. Cancers (Basel) 2020; 12:cancers12123574. [PMID: 33265926 PMCID: PMC7760033 DOI: 10.3390/cancers12123574] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Recently, immunotherapy has presented new opportunities for clinical development in the treatment of non-small cell lung cancer (NSCLC). Although effective in sustaining overall survival in several clinical trials, not all the NSCLC patients respond to these treatments. Thus, a better patient selection, as well as the identification of predictive biomarkers of treatment efficacy, are of paramount importance. In this work, metabolomics was used with the aim of identifying responder with respect to non-responder subjects. We show that the metabolomic fingerprint of serum samples, collected before therapy, acts as a predictive biomarker to treatment response. Prospective identification of subjects that will benefit from immunotherapy could improve patient stratification, thus optimizing the treatment and avoiding unsuccessful strategies. Abstract In the treatment of advanced non-small cell lung cancer (NSCLC), immune checkpoint inhibitors have shown remarkable results. However, not all patients with NSCLC respond to this drug treatment or receive durable benefits. Thus, patient stratification and selection, as well as the identification of predictive biomarkers, represent pivotal aspects to address. In this framework, metabolomics can be used to support the discrimination between responders and non-responders. Here, metabolomics was used to analyze the sera samples from 50 patients with NSCL treated with immune checkpoint inhibitors. All the samples were collected before the beginning of the treatment and were analyzed by NMR spectroscopy and multivariate statistical analyses. Significantly, we show that the metabolomic fingerprint of serum acts as a predictive “collective” biomarker to immune checkpoint inhibitors response, being able to predict individual therapy outcome with > 80% accuracy. Metabolomics represents a potential strategy for the real-time selection and monitoring of patients treated with immunotherapy. The prospective identification of responders and non-responders could improve NSCLC treatment and patient stratification, thus avoiding ineffective therapeutic strategies.
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Affiliation(s)
- Veronica Ghini
- Cirmmp, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy;
- Magnetic Resonance Center, CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy;
| | - Letizia Laera
- Sandro Pitigliani, Department of Medical Oncology, Hospital of Prato, via Suor Niccolina Infermiera, 20/22, 59100 Prato, Italy; (L.L.); (B.F.); (F.d.M.); (A.M.)
- Department of Oncology, Miulli hospital, Acquaviva delle Fonti, 70021 Bari, Italy
| | - Beatrice Fantechi
- Sandro Pitigliani, Department of Medical Oncology, Hospital of Prato, via Suor Niccolina Infermiera, 20/22, 59100 Prato, Italy; (L.L.); (B.F.); (F.d.M.); (A.M.)
| | - Francesca del Monte
- Sandro Pitigliani, Department of Medical Oncology, Hospital of Prato, via Suor Niccolina Infermiera, 20/22, 59100 Prato, Italy; (L.L.); (B.F.); (F.d.M.); (A.M.)
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, via Suor Niccolina Infermiera, 20/22, 59100 Prato, Italy;
| | - Amelia McCartney
- Sandro Pitigliani, Department of Medical Oncology, Hospital of Prato, via Suor Niccolina Infermiera, 20/22, 59100 Prato, Italy; (L.L.); (B.F.); (F.d.M.); (A.M.)
| | - Leonardo Tenori
- Magnetic Resonance Center, CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy;
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center, CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy;
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
- Correspondence: (C.L.); (D.P.); Tel.: +39-0554-574-296 (C.L.); +39-0574-802-520 (D.P.)
| | - Daniele Pozzessere
- Sandro Pitigliani, Department of Medical Oncology, Hospital of Prato, via Suor Niccolina Infermiera, 20/22, 59100 Prato, Italy; (L.L.); (B.F.); (F.d.M.); (A.M.)
- Correspondence: (C.L.); (D.P.); Tel.: +39-0554-574-296 (C.L.); +39-0574-802-520 (D.P.)
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27
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Ghini V, Tenori L, Pane M, Amoruso A, Marroncini G, Squarzanti DF, Azzimonti B, Rolla R, Savoia P, Tarocchi M, Galli A, Luchinat C. Effects of Probiotics Administration on Human Metabolic Phenotype. Metabolites 2020; 10:metabo10100396. [PMID: 33036487 PMCID: PMC7601401 DOI: 10.3390/metabo10100396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
The establishment of the beneficial interactions between the host and its microbiota is essential for the correct functioning of the organism, since microflora alterations can lead to many diseases. Probiotics improve balanced microbial communities, exerting substantial health-promoting effects. Here we monitored the molecular outcomes, obtained by gut microflora modulation through probiotic treatment, on human urine and serum metabolic profiles, with a metabolomic approach. Twenty-two subjects were enrolled in the study and administered with two different probiotic types, both singularly and in combination, for 8 weeks. Urine and serum samples were collected before and during the supplementation and were analyzed by nuclear magnetic resonance (NMR) spectroscopy and statistical analyses. After eight weeks of treatment, probiotics deeply influence the urinary metabolic profiles of the volunteers, without significantly altering their single phenotypes. Anyway, bacteria supplementation tends to reduce the differences in metabolic phenotypes among individuals. Overall, the effects are recipient-dependent, and in some individuals, robust effects are already well visible after four weeks. Modifications in metabolite levels, attributable to each type of probiotic administration, were also monitored. Metabolomic analysis of biofluids turns out to be a powerful technique to monitor the dynamic interactions between the microflora and the host, and the individual response to probiotic assumption.
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Affiliation(s)
- Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy;
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy;
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Marco Pane
- Probiotical S.p.A., 28100 Novara, Italy; (M.P.); (A.A.)
| | | | - Giada Marroncini
- Department of Experimental and Clinical Biochemical Sciences “Mario Serio”, University of Florence, 50100 Firenze, Italy; (G.M.); (M.T.); (A.G.)
| | - Diletta Francesca Squarzanti
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Via Solaroli 17, 28100 Novara, Italy; (D.F.S.); (B.A.); (R.R.); (P.S.)
- Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), DiSS, UPO, Corso Trieste 15/A, 28100 Novara, Italy
| | - Barbara Azzimonti
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Via Solaroli 17, 28100 Novara, Italy; (D.F.S.); (B.A.); (R.R.); (P.S.)
- Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), DiSS, UPO, Corso Trieste 15/A, 28100 Novara, Italy
| | - Roberta Rolla
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Via Solaroli 17, 28100 Novara, Italy; (D.F.S.); (B.A.); (R.R.); (P.S.)
- Clinical Chemistry Unit, Azienda Ospedaliero Universitaria Maggiore della Carità, Corso Mazzini 18, 28100 Novara, Italy
| | - Paola Savoia
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Via Solaroli 17, 28100 Novara, Italy; (D.F.S.); (B.A.); (R.R.); (P.S.)
- SCDU Dermatology, AOU Maggiore della Carità, 28100 Novara, Italy
| | - Mirko Tarocchi
- Department of Experimental and Clinical Biochemical Sciences “Mario Serio”, University of Florence, 50100 Firenze, Italy; (G.M.); (M.T.); (A.G.)
| | - Andrea Galli
- Department of Experimental and Clinical Biochemical Sciences “Mario Serio”, University of Florence, 50100 Firenze, Italy; (G.M.); (M.T.); (A.G.)
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy;
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: ; Tel.: +39-055-457-4296
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Li W, Zhao F, Pan J, Qu H. Influence of ethanol concentration of extraction solvent on metabolite profiling for Salviae Miltiorrhizae Radix et Rhizoma extract by 1H NMR spectroscopy and multivariate data analysis. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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29
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Liu Y, Du Q, Sun D, Han R, Teng M, Chen S, You H, Dong Y. Clinical applications of circulating tumor DNA in monitoring breast cancer drug resistance. Future Oncol 2020; 16:2863-2878. [PMID: 32976028 DOI: 10.2217/fon-2019-0760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is one of the leading causes of cancer-related deaths in women worldwide. Unfortunately, treatments often fail because of the development of drug resistance, the underlying mechanisms of which remain unclear. Circulating tumor DNA (ctDNA) is free DNA released into the blood by necrosis, apoptosis or direct secretion by tumor cells. In contrast to repeated, highly invasive tumor biopsies, ctDNA reflects all molecular alterations of tumors dynamically and captures both spatial and temporal tumor heterogeneity. Highly sensitive technologies, including personalized digital PCR and deep sequencing, make it possible to monitor response to therapies, predict drug resistance and tailor treatment regimens by identifying the genomic alteration profile of ctDNA, thereby achieving precision medicine. This review focuses on the current status of ctDNA biology, the technologies used to detect ctDNA and the potential clinical applications of identifying drug resistance mechanisms by detecting tumor-specific genomic alterations in breast cancer.
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Affiliation(s)
- Yang Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Qian Du
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Dan Sun
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Ruiying Han
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Mengmeng Teng
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Siying Chen
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Haisheng You
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Yalin Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
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30
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Gómez-Cebrián N, García-Flores M, Rubio-Briones J, López-Guerrero JA, Pineda-Lucena A, Puchades-Carrasco L. Targeted Metabolomics Analyses Reveal Specific Metabolic Alterations in High-Grade Prostate Cancer Patients. J Proteome Res 2020; 19:4082-4092. [PMID: 32924497 DOI: 10.1021/acs.jproteome.0c00493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prostate cancer (PCa) is a hormone-dependent tumor characterized by an extremely heterogeneous prognosis. Despite recent advances in partially uncovering some of the biological processes involved in its progression, there is still an urgent need for identifying more accurate and specific prognostic procedures to differentiate between disease stages. In this context, targeted approaches, focused on mapping dysregulated metabolic pathways, could play a critical role in identifying the mechanisms driving tumorigenesis and metastasis. In this study, a targeted analysis of the nuclear magnetic resonance-based metabolomic profile of PCa patients with different tumor grades, guided by transcriptomics profiles associated with their stages, was performed. Serum and urine samples were collected from 73 PCa patients. Samples were classified according to their Gleason score (GS) into low-GS (GS < 7) and high-GS PCa (GS ≥ 7) groups. A total of 36 metabolic pathways were found to be dysregulated in the comparison between different PCa grades. Particularly, the levels of glucose, glycine and 1-methlynicotinamide, metabolites involved in energy metabolism and nucleotide synthesis were significantly altered between both groups of patients. These results underscore the potential of targeted metabolomic profiling to characterize relevant metabolic changes involved in the progression of this neoplastic process.
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Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain.,Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología (FIVO), Valencia 46009, Spain
| | - María García-Flores
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología (FIVO), Valencia 46009, Spain.,IVO-CIPF Joint Research Unit of Cancer, Príncipe Felipe Research Centre (CIPF), Valencia 46012, Spain
| | - José Rubio-Briones
- Department of Urology, Fundación Instituto Valenciano de Oncología (FIVO), Valencia 46009, Spain
| | - José Antonio López-Guerrero
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología (FIVO), Valencia 46009, Spain.,IVO-CIPF Joint Research Unit of Cancer, Príncipe Felipe Research Centre (CIPF), Valencia 46012, Spain.,Department of Basic Medical Sciences, School of Medicine, Catholic University of Valencia 'San Vicente Martir', Valencia 46001, Spain
| | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain.,Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, Navarra 31008, Spain
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Antonaros F, Ghini V, Pulina F, Ramacieri G, Cicchini E, Mannini E, Martelli A, Feliciello A, Lanfranchi S, Onnivello S, Vianello R, Locatelli C, Cocchi G, Pelleri MC, Vitale L, Strippoli P, Luchinat C, Turano P, Piovesan A, Caracausi M. Plasma metabolome and cognitive skills in Down syndrome. Sci Rep 2020; 10:10491. [PMID: 32591596 PMCID: PMC7319960 DOI: 10.1038/s41598-020-67195-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Trisomy 21 (Down syndrome, DS) is the main human genetic cause of intellectual disability (ID). Lejeune hypothesized that DS could be considered a metabolic disease, and we found that subjects with DS have a specific plasma and urinary metabolomic profile. In this work we confirmed the alteration of mitochondrial metabolism in DS and also investigated if metabolite levels are related to cognitive aspects of DS. We analyzed the metabolomic profiles of plasma samples from 129 subjects with DS and 46 healthy control (CTRL) subjects by 1H Nuclear Magnetic Resonance (NMR). Multivariate analysis of the NMR metabolomic profiles showed a clear discrimination (up to 94% accuracy) between the two groups. The univariate analysis revealed a significant alteration in 7 metabolites out of 28 assigned unambiguously. Correlations among the metabolite levels in DS and CTRL groups were separately investigated and statistically significant relationships appeared. On the contrary, statistically significant correlations among the NMR-detectable part of DS plasma metabolome and the different intelligence quotient ranges obtained by Griffiths-III or WPPSI-III tests were not found. Even if metabolic imbalance provides a clear discrimination between DS and CTRL groups, it appears that the investigated metabolomic profiles cannot be associated with the degree of ID.
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Affiliation(s)
- Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Veronica Ghini
- CIRMMP, Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, FI, Italy
| | - Francesca Pulina
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Giuseppe Ramacieri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Elena Cicchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Elisa Mannini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Anna Martelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Agnese Feliciello
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Silvia Lanfranchi
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Sara Onnivello
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Renzo Vianello
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Claudio Luchinat
- CERM, Center of Magnetic Resonance and Department of Chemistry, University of Florence, via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- CERM, Center of Magnetic Resonance and Department of Chemistry, University of Florence, via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
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32
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Nannini G, Meoni G, Amedei A, Tenori L. Metabolomics profile in gastrointestinal cancers: Update and future perspectives. World J Gastroenterol 2020; 26:2514-2532. [PMID: 32523308 PMCID: PMC7265149 DOI: 10.3748/wjg.v26.i20.2514] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
Despite recent progress in diagnosis and therapy, gastrointestinal (GI) cancers remain one of the most important causes of death with a poor prognosis due to late diagnosis. Serum tumor markers and detection of occult blood in the stool are the current tests used in the clinic of GI cancers; however, these tests are not useful as diagnostic screening since they have low specificity and low sensitivity. Considering that one of the hallmarks of cancer is dysregulated metabolism and metabolomics is an optimal approach to illustrate the metabolic mechanisms that belong to living systems, is now clear that this -omics could open a new way to study cancer. In the last years, nuclear magnetic resonance (NMR) metabolomics has demonstrated to be an optimal approach for diseases' diagnosis nevertheless a few studies focus on the NMR capability to find new biomarkers for early diagnosis of GI cancers. For these reasons in this review, we will give an update on the status of NMR metabolomic studies for the diagnosis and development of GI cancers using biological fluids.
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Affiliation(s)
- Giulia Nannini
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Gaia Meoni
- Giotto Biotech Srl, and CERM (University of Florence), Florence 50019, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
- SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera Universitaria Careggi, Florence 50134, Italy
| | - Leonardo Tenori
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Florence 50019, Italy
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33
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Kim J, Ahn JK, Cheong YE, Lee SJ, Cha HS, Kim KH. Systematic re-evaluation of the long-used standard protocol of urease-dependent metabolome sample preparation. PLoS One 2020; 15:e0230072. [PMID: 32182259 PMCID: PMC7077817 DOI: 10.1371/journal.pone.0230072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/20/2020] [Indexed: 11/24/2022] Open
Abstract
In the urinary metabolomics for finding biomarkers in urine, owing to high concentrations of urea, for chromatography-based metabolomic analysis, urea needed to be degraded by urease. This urease pretreatment has been the key step of sample preparation for standard urinary metabolomics until today even for mass spectrometry-based analysis. The urease pretreatment involving incubation of urine with urease contradicts the concept of metabolome sampling, which should immediately arrest metabolic reactions to prevent alterations of a metabolite profile. Nonetheless, the impact of urease pretreatment has not been clearly elucidated yet. We found that activities of urease and endogenous urinary enzymes and metabolite contaminants from the urease preparations introduce artefacts into metabolite profiles, thus leading to misinterpretation.
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Affiliation(s)
- Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Joong Kyong Ahn
- Division of Rheumatology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yu Eun Cheong
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Sung-Joon Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hoon-Suk Cha
- Division of Rheumatology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- * E-mail: (KHK); (HSC)
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
- * E-mail: (KHK); (HSC)
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34
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Vignoli A, Paciotti S, Tenori L, Eusebi P, Biscetti L, Chiasserini D, Scheltens P, Turano P, Teunissen C, Luchinat C, Parnetti L. Fingerprinting Alzheimer's Disease by 1H Nuclear Magnetic Resonance Spectroscopy of Cerebrospinal Fluid. J Proteome Res 2020; 19:1696-1705. [PMID: 32118444 DOI: 10.1021/acs.jproteome.9b00850] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this study, we sought for a cerebrospinal fluid (CSF) metabolomic fingerprint in Alzheimer's disease (AD) patients characterized, according to the clinical picture and CSF AD core biomarkers (Aβ42, p-tau, and t-tau), both at pre-dementia (mild cognitive impairment due to AD, MCI-AD) and dementia stages (ADdem) and in a group of patients with a normal CSF biomarker profile (non-AD) using untargeted 1H nuclear magnetic resonance (NMR) spectroscopy-based metabolomics. This is a retrospective study based on two independent cohorts: a Dutch cohort, which comprises 20 ADdem, 20 MCI-AD, and 20 non-AD patients, and an Italian cohort, constituted by 14 ADdem and 12 non-AD patients. 1H NMR CSF spectra were analyzed using OPLS-DA. Metabolomic fingerprinting in the Dutch cohort provides a significant discrimination (86.1% accuracy) between ADdem and non-AD. MCI-AD patients show a good discrimination with respect to ADdem (70.0% accuracy) but only slight differences when compared with non-AD (59.6% accuracy). Acetate, valine, and 3-hydroxyisovalerate result to be altered in ADdem patients. Valine correlates with cognitive decline at follow-up (R = 0.53, P = 0.0011). The discrimination between ADdem and non-AD was confirmed in the Italian cohort. The CSF metabolomic fingerprinting shows a signature characteristic of ADdem patients with respect to MCI-AD and non-AD patients.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino 50019, Italy
| | - Silvia Paciotti
- Laboratory of Clinical Neurochemistry, Department of Medicine, Section of Neurology, University of Perugia, Perugia 06123, Italy.,Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, Perugia 06123, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino 50019, Italy
| | - Paolo Eusebi
- Laboratory of Clinical Neurochemistry, Department of Medicine, Section of Neurology, University of Perugia, Perugia 06123, Italy
| | - Leonardo Biscetti
- Laboratory of Clinical Neurochemistry, Department of Medicine, Section of Neurology, University of Perugia, Perugia 06123, Italy
| | - Davide Chiasserini
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, Perugia 06123, Italy
| | - Philip Scheltens
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
| | - Charlotte Teunissen
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Sesto Fiorentino 50019, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
| | - Lucilla Parnetti
- Laboratory of Clinical Neurochemistry, Department of Medicine, Section of Neurology, University of Perugia, Perugia 06123, Italy
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35
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Missailidis D, Sanislav O, Allan CY, Annesley SJ, Fisher PR. Cell-Based Blood Biomarkers for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Int J Mol Sci 2020; 21:ijms21031142. [PMID: 32046336 PMCID: PMC7037777 DOI: 10.3390/ijms21031142] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a devastating illness whose biomedical basis is now beginning to be elucidated. We reported previously that, after recovery from frozen storage, lymphocytes (peripheral blood mononuclear cells, PBMCs) from ME/CFS patients die faster in culture medium than those from healthy controls. We also found that lymphoblastoid cell lines (lymphoblasts) derived from these PBMCs exhibit multiple abnormalities in mitochondrial respiratory function and signalling activity by the cellular stress-sensing kinase Target Of Rapamycin Complex 1 (TORC1). These differences were correlated with disease severity, as measured by the Richardson and Lidbury weighted standing test. The clarity of the differences between these cells derived from ME/CFS patient blood and those from healthy controls suggested that they may provide useful biomarkers for ME/CFS. Here, we report a preliminary investigation into that possibility using a variety of analytical classification tools, including linear discriminant analysis, logistic regression and receiver operating characteristic (ROC) curve analysis. We found that results from three different tests—lymphocyte death rate, mitochondrial respiratory function and TORC1 activity—could each individually serve as a biomarker with better than 90% sensitivity but only modest specificity vís a vís healthy controls. However, in combination, they provided a cell-based biomarker with sensitivity and specificity approaching 100% in our sample. This level of sensitivity and specificity was almost equalled by a suggested protocol in which the frozen lymphocyte death rate was used as a highly sensitive test to triage positive samples to the more time consuming and expensive tests measuring lymphoblast respiratory function and TORC1 activity. This protocol provides a promising biomarker that could assist in more rapid and accurate diagnosis of ME/CFS.
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Effect of Estrogen Receptor Status on Circulatory Immune and Metabolomics Profiles of HER2-Positive Breast Cancer Patients Enrolled for Neoadjuvant Targeted Chemotherapy. Cancers (Basel) 2020; 12:cancers12020314. [PMID: 32013102 PMCID: PMC7072610 DOI: 10.3390/cancers12020314] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
HER2-positive breast cancer (BC) represents a heterogeneous cancer disease. In an attempt to identify new stratification models useful for prognosis and therapeutic strategy, we investigated the influence of estrogen receptor (ER) status on the host immune and metabolomics profile of HER2-positive BC patients enrolled for neoadjuvant targeted chemotherapy (NATC). The study enrolled 43 HER2-positive BC patients eligible for NATC based on the trastuzumab-paclitaxel combination. Baseline circulatory cytokines and 1H NMR plasma metabolomics profiles were investigated. Differences in the immune cytokines and metabolomics profile as a function of the ER status, and their association with clinical outcomes were studied by multivariate and univariate analysis. Baseline metabolomics profiles were found to discriminate HER2-positive ER(+) from ER(−) BC patients. Within the ER(+) group an immune-metabolomics model, based on TNF-α and valine, predicted pathological complete response to NATC with 90.9% accuracy (AUROC = 0.92, p = 0.004). Moreover, metabolomics information integrated with IL-2 and IL-10 cytokine levels were prognostic of relapse with an accuracy of 95.5%. The results indicate that in HER2-positive BC patients the ER status influences the host circulatory immune-metabolomics profile. The baseline immune-metabolomics assessment in combination with ER status could represent an independent stratification tool able to predict NATC response and disease relapse of HER2-positive patients.
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DHA-Induced Perturbation of Human Serum Metabolome. Role of the Food Matrix and Co-Administration of Oat β-glucan and Anthocyanins. Nutrients 2019; 12:nu12010086. [PMID: 31892215 PMCID: PMC7019822 DOI: 10.3390/nu12010086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 12/16/2022] Open
Abstract
Docosahexaenoic acid (DHA) has been reported to have a positive impact on many diet-related disease risks, including metabolic syndrome. Although many DHA-enriched foods have been marketed, the impact of different food matrices on the effect of DHA is unknown. As well, the possibility to enhance DHA effectiveness through the co-administration of other bioactives has seldom been considered. We evaluated DHA effects on the serum metabolome administered to volunteers at risk of metabolic syndrome as an ingredient of three different foods. Foods were enriched with DHA alone or in combination with oat beta-glucan or anthocyanins and were administered to volunteers for 4 weeks. Serum samples collected at the beginning and end of the trial were analysed by NMR-based metabolomics. Multivariate and univariate statistical analyses were used to characterize modifications in the serum metabolome and to evaluate bioactive-bioactive and bioactive-food matrix interactions. DHA administration induces metabolome perturbation that is influenced by the food matrix and the co-presence of other bioactives. In particular, when co-administered with oat beta-glucan, DHA induces a strong rearrangement in the lipoprotein profile of the subjects. The observed modifications are consistent with clinical results and indicate that metabolomics represents a possible strategy to choose the most appropriate food matrices for bioactive enrichment.
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Flügge F, Figge L, Duhm-Harbeck P, Kammler R, Habermann JK. How clinical biobanks can support precision medicine: from standardized preprocessing to treatment guidance. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019. [DOI: 10.1080/23808993.2019.1690395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Friedemann Flügge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | - Lena Figge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | | | - Rosita Kammler
- Translational Research Coordination for International Breast Cancer Study Group and European Thoracic Oncology Platform, Bern, Switzerland
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
| | - Jens K. Habermann
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein (UKSH), Lübeck, Germany
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Wang X, Gu H, Palma-Duran SA, Fierro A, Jasbi P, Shi X, Bresette W, Tasevska N. Influence of Storage Conditions and Preservatives on Metabolite Fingerprints in Urine. Metabolites 2019; 9:metabo9100203. [PMID: 31569767 PMCID: PMC6836253 DOI: 10.3390/metabo9100203] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
Human urine, which is rich in metabolites, provides valuable approaches for biomarker measurement. Maintaining the stability of metabolites in urine is critical for accurate and reliable research results and subsequent interpretation. In this study, the effect of storage temperature (4, 22, and 40 °C), storage time (24 and 48 h), and use of preservatives (boric acid (BA), thymol) and para-aminobenzoic acid (PABA) on urinary metabolites in the pooled urine samples from 20 participants was systematically investigated using large-scale targeted liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomics. Statistical analysis of 158 reliably detected metabolites showed that metabolites in urine with no preservative remained stable at 4 °C for 24 and 48 h as well as at 22 °C for 24 h, but significant metabolite differences were observed in urine stored at 22 °C for 48 h and at 40 °C. The mere addition of BA caused metabolite changes. Thymol was observed to be effective in maintaining metabolite stability in urine in all the conditions designed, most likely due to the inhibitory effect of thymol on urine microbiota. Our results provide valuable urine preservation guidance during sample storage, which is essential for obtaining reliable, accurate, and reproducible analytical results from urine samples.
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Affiliation(s)
- Xinchen Wang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | | | - Andres Fierro
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Xiaojian Shi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - William Bresette
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Natasha Tasevska
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
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