1
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Woo H, Park J, Kim KH, Ku JY, Ha HK, Cho Y. Alix-normalized exosomal programmed death-ligand 1 analysis in urine enables precision monitoring of urothelial cancer. Cancer Sci 2024; 115:1602-1610. [PMID: 38480462 PMCID: PMC11093207 DOI: 10.1111/cas.16106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/23/2024] [Accepted: 01/28/2024] [Indexed: 05/15/2024] Open
Abstract
Anti-programmed death-ligand 1 (PD-L1) Ab-based therapies have demonstrated potential for treating metastatic urothelial cancer with high PD-L1 expression. Urinary exosomes are promising biomarkers for liquid biopsy, but urine's high variability requires normalization for accurate analysis. This study proposes using the PD-L1/Alix ratio to normalize exosomal PD-L1 signal intensity with Alix, an internal exosomal protein less susceptible to heterogeneity concerns than surface protein markers. Extracellular vesicles were isolated using ExoDisc and characterized using various methods, including ExoView to analyze tetraspanins, PD-L1, and Alix on individual exosomes. On-disc ELISA was used to evaluate PD-L1 and Alix-normalized PD-L1 in 15 urothelial cancer patients during the initial treatment cycle with Tecentriq. Results showed that Alix signal range was relatively uniform, whereas tetraspanin marker intensity varied for individual exosome particles. On-disc ELISA was more reliable for detecting exosomal PD-L1 expression than standard plate ELISA-based measurement. Using exosomal Alix expression for normalization is a more reliable approach than conventional methods for monitoring patient status. Overall, the study provides a practical and reliable method for detecting exosomal PD-L1 in urine samples from patients with urothelial cancer.
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Affiliation(s)
- Hyun‐Kyung Woo
- Center for Soft and Living MatterInstitute for Basic Science (IBS)UlsanSouth Korea
- Department of Biomedical EngineeringUlsan National Institute of Science and Technology (UNIST)UlsanSouth Korea
- Present address:
Center for Systems Biology, Massachusetts General HospitalHarvard Medical SchoolBostonMassachusettsMAUSA
| | - Juhee Park
- Center for Soft and Living MatterInstitute for Basic Science (IBS)UlsanSouth Korea
| | - Kyung Hwan Kim
- Biomedical Research InstitutePusan National University HospitalBusanSouth Korea
- Department of Urology, Pusan National University HospitalCollege of Medicine, Pusan National UniversityBusanSouth Korea
| | - Ja Yoon Ku
- Biomedical Research InstitutePusan National University HospitalBusanSouth Korea
- Department of Urology, Pusan National University HospitalCollege of Medicine, Pusan National UniversityBusanSouth Korea
- Present address:
Dongnam Institute of Radiological and Medical Sciences Cancer CenterBusanSouth Korea
| | - Hong Koo Ha
- Biomedical Research InstitutePusan National University HospitalBusanSouth Korea
- Department of Urology, Pusan National University HospitalCollege of Medicine, Pusan National UniversityBusanSouth Korea
| | - Yoon‐Kyoung Cho
- Center for Soft and Living MatterInstitute for Basic Science (IBS)UlsanSouth Korea
- Department of Biomedical EngineeringUlsan National Institute of Science and Technology (UNIST)UlsanSouth Korea
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2
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Brix F, Demetrowitsch T, Jensen-Kroll J, Zacharias HU, Szymczak S, Laudes M, Schreiber S, Schwarz K. Evaluating the Effect of Data Merging and Postacquisition Normalization on Statistical Analysis of Untargeted High-Resolution Mass Spectrometry Based Urinary Metabolomics Data. Anal Chem 2024; 96:33-40. [PMID: 38113356 DOI: 10.1021/acs.analchem.3c01380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Urine is one of the most widely used biofluids in metabolomic studies because it can be collected noninvasively and is available in large quantities. However, it shows large heterogeneity in sample concentration and consequently requires normalization to reduce unwanted variation and extract meaningful biological information. Biological samples like urine are commonly measured with electrospray ionization (ESI) coupled to a mass spectrometer, producing data sets for positive and negative modes. Combining these gives a more complete picture of the total metabolites present in a sample. However, the effect of this data merging on subsequent data analysis, especially in combination with normalization, has not yet been analyzed. To address this issue, we conducted a neutral comparison study to evaluate the performance of eight postacquisition normalization methods under different data merging procedures using 1029 urine samples from the Food Chain plus (FoCus) cohort. Samples were measured with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Normalization methods were evaluated by five criteria capturing the ability to remove sample concentration variation and preserve relevant biological information. Merging data after normalization was generally favorable for quality control (QC) sample similarity, sample classification, and feature selection for most of the tested normalization methods. Merging data after normalization and the usage of probabilistic quotient normalization (PQN) in a similar setting are generally recommended. Relying on a single analyte to capture sample concentration differences, like with postacquisition creatinine normalization, seems to be a less preferable approach, especially when data merging is applied.
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Affiliation(s)
- Fynn Brix
- Institute of Human Nutrition and Food Science, Kiel University, Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Tobias Demetrowitsch
- Institute of Human Nutrition and Food Science, Kiel University, Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Julia Jensen-Kroll
- Institute of Human Nutrition and Food Science, Kiel University, Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Helena U Zacharias
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, 30625 Hannover, Germany
- Department of Internal Medicine I, University Medical Centre Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Silke Szymczak
- Institute of Medical Biometry and Statistics, University of Luebeck and Medical Centre Schleswig-Holstein, Campus Luebeck, 23562 Luebeck, Germany
| | - Matthias Laudes
- Department of Internal Medicine I, University Medical Centre Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Diabetes and Clinical Metabolic Research, Kiel University, Düsternbrooker Weg 17, 24105 Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Centre Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Diabetes and Clinical Metabolic Research, Kiel University, Düsternbrooker Weg 17, 24105 Kiel, Germany
| | - Karin Schwarz
- Institute of Human Nutrition and Food Science, Kiel University, Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
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3
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Mervant L, Tremblay-Franco M, Olier M, Jamin E, Martin JF, Trouilh L, Buisson C, Naud N, Maslo C, Héliès-Toussaint C, Fouché E, Kesse-Guyot E, Hercberg S, Galan P, Deschasaux-Tanguy M, Touvier M, Pierre F, Debrauwer L, Guéraud F. Urinary Metabolome Analysis Reveals Potential Microbiota Alteration and Electrophilic Burden Induced by High Red Meat Diet: Results from the French NutriNet-Santé Cohort and an In Vivo Intervention Study in Rats. Mol Nutr Food Res 2023; 67:e2200432. [PMID: 36647294 DOI: 10.1002/mnfr.202200432] [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: 07/01/2022] [Revised: 11/22/2022] [Indexed: 01/18/2023]
Abstract
SCOPE High red and processed meat consumption is associated with several adverse outcomes such as colorectal cancer and overall global mortality. However, the underlying mechanisms remain debated and need to be elucidated. METHODS AND RESULTS Urinary untargeted Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics data from 240 subjects from the French cohort NutriNet-Santé are analyzed. Individuals are matched and divided into three groups according to their consumption of red and processed meat: high red and processed meat consumers, non-red and processed meat consumers, and at random group. Results are supported by a preclinical experiment where rats are fed either a high red meat or a control diet. Microbiota derived metabolites, in particular indoxyl sulfate and cinnamoylglycine, are found impacted by the high red meat diet in both studies, suggesting a modification of microbiota by the high red/processed meat diet. Rat microbiota sequencing analysis strengthens this observation. Although not evidenced in the human study, rat mercapturic acid profile concomitantly reveals an increased lipid peroxidation induced by high red meat diet. CONCLUSION Novel microbiota metabolites are identified as red meat consumption potential biomarkers, suggesting a deleterious effect, which could partly explain the adverse effects associated with high red and processed meat consumption.
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Affiliation(s)
- Loïc Mervant
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
| | - Marie Tremblay-Franco
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - Maïwenn Olier
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France
| | - Emilien Jamin
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - Jean-Francois Martin
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - Lidwine Trouilh
- Plateforme Genome et Transcriptome (GeT-Biopuces), Toulouse Biotechnology Institute (TBI), Université ide Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, Toulouse, F-31077, France
| | - Charline Buisson
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
| | - Nathalie Naud
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
| | - Claire Maslo
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France
| | - Cécile Héliès-Toussaint
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
| | - Edwin Fouché
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
| | - Emmanuelle Kesse-Guyot
- French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France.,Sorbonne Paris Nord University, INSERM U1153, INRAe U1125, CNAM, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 74 rue Marcel Cachin, Bobigny, 93017, France
| | - Serge Hercberg
- French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France.,Sorbonne Paris Nord University, INSERM U1153, INRAe U1125, CNAM, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 74 rue Marcel Cachin, Bobigny, 93017, France
| | - Pilar Galan
- Sorbonne Paris Nord University, INSERM U1153, INRAe U1125, CNAM, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 74 rue Marcel Cachin, Bobigny, 93017, France
| | - Mélanie Deschasaux-Tanguy
- French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France.,Sorbonne Paris Nord University, INSERM U1153, INRAe U1125, CNAM, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 74 rue Marcel Cachin, Bobigny, 93017, France
| | - Mathilde Touvier
- French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France.,Sorbonne Paris Nord University, INSERM U1153, INRAe U1125, CNAM, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center - University of Paris (CRESS), 74 rue Marcel Cachin, Bobigny, 93017, France
| | - Fabrice Pierre
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
| | - Laurent Debrauwer
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - Francoise Guéraud
- Toxalim, Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France.,French Network for Nutrition and Cancer Research (NACRe Network), Jouy-en-Josas, 78352, France
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4
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Changes in the Urine Metabolomic Profile in Patients Recovering from Severe COVID-19. Metabolites 2023; 13:metabo13030364. [PMID: 36984804 PMCID: PMC10058594 DOI: 10.3390/metabo13030364] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Metabolomics is a relatively new research area that focuses mostly on the profiling of selected molecules and metabolites within the organism. A SARS-CoV-2 infection itself can lead to major disturbances in the metabolite profile of the infected individuals. The aim of this study was to analyze metabolomic changes in the urine of patients during the acute phase of COVID-19 and approximately one month after infection in the recovery period. We discuss the observed changes in relation to the alterations resulting from changes in the blood plasma metabolome, as described in our previous study. The metabolome analysis was performed using NMR spectroscopy from the urine of patients and controls. The urine samples were collected at three timepoints, namely upon hospital admission, during hospitalization, and after discharge from the hospital. The acute COVID-19 phase induced massive alterations in the metabolic composition of urine was linked with various changes taking place in the organism. Discriminatory analyses showed the feasibility of successful discrimination of COVID-19 patients from healthy controls based on urinary metabolite levels, with the highest significance assigned to citrate, Hippurate, and pyruvate. Our results show that the metabolomic changes persist one month after the acute phase and that the organism is not fully recovered.
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5
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Rhodes AML, Ali S, Minnion M, Lee LH, Joseph BM, Ndzo J, Clarke NMP, Feelisch M, Aarvold A. An Explorative Study into the Aetiology of Developmental Dysplasia of the Hip Using Targeted Urine Metabolomics. Antioxidants (Basel) 2023; 12:antiox12030538. [PMID: 36978785 PMCID: PMC10045260 DOI: 10.3390/antiox12030538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
Developmental dysplasia of the hip (DDH) is the most prevalent congenital musculoskeletal disorder, yet its cause remains unknown. Adequate nutrient provision and coordinated electron exchange (redox) processes are critical for foetal growth and tissue development. This novel study sought to explore specific biochemical pathways in skeletal development for potential involvement in the aetiology of DDH. Spot urine samples were collected from infants, aged 13–61 days, with and without DDH. Ion chromatography-mass spectrometry was used to quantify thiosulphate, sulphate, nitrate, and phosphate, whilst nitrite was quantified using high-performance liquid chromato-graphy. Thiobarbituric acid reactive substances (TBARS) were measured as markers of lipid peroxidation. Creatinine and osmolality were determined by a 96-well plate assay and micro-osmometer to potentially normalise values for renal function, lean body mass, and hydration status. Urine samples were analysed from 99 babies: 30 with DDH and 69 age-matched non-DDH controls. Thiosulphate, TBARS, and creatinine concentrations differed between the DDH group and the controls (p = 0.025, 0.015, and 0.004 respectively). Urine osmolality was significantly lower in DDH compared to the controls (p = 0.036), indicative of the production of a more diluted urine in DDH infants. Following adjustment for osmolality, significant differences became apparent in urinary sulphate levels in DDH (p = 0.035) whereas all other parameters were similar between the groups. This is the first study to assess the potential role of these inorganic anions in DDH. The higher levels of sulphate found in infants with DDH suggests either enhanced intake from milk, increased endogenous formation, or impaired renal reabsorption. This investigation demonstrates the power of urine metabolomics and highlights the importance of normalisation for hydration status to disentangle developmental disorders. Our results strongly suggest that DDH is a systemic disease associated with altered uptake, formation, or handling of sulphate. There is potential for new opportunities in the prevention or treatment of DDH via nutritional intervention.
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Affiliation(s)
- Amanda M. L. Rhodes
- Orthopaedic Surgery, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Sehrish Ali
- Clinical and Experimental Sciences, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Magdalena Minnion
- Clinical and Experimental Sciences, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Ling H. Lee
- Southampton Children’s Hospital, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Brijil M. Joseph
- Southampton Children’s Hospital, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Judwin Ndzo
- Southampton Children’s Hospital, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Nicholas M. P. Clarke
- Department of Paediatric Orthopaedics, University of Southampton, Southampton SO16 6YD, UK
| | - Martin Feelisch
- Clinical and Experimental Sciences, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, UK
- Correspondence: (M.F.); (A.A.)
| | - Alexander Aarvold
- Southampton Children’s Hospital, University Hospital Southampton, Southampton SO16 6YD, UK
- Correspondence: (M.F.); (A.A.)
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6
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Saade MC, Clark AJ, Parikh SM. States of quinolinic acid excess in urine: A systematic review of human studies. Front Nutr 2022; 9:1070435. [PMID: 36590198 PMCID: PMC9800835 DOI: 10.3389/fnut.2022.1070435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Quinolinic acid is an intermediate compound derived from the metabolism of dietary tryptophan. Its accumulation has been reported in patients suffering a broad spectrum of diseases and conditions. In this manuscript, we present the results of a systematic review of research studies assessing urinary quinolinic acid in health and disease. Methods We performed a literature review using PubMed, Cochrane, and Scopus databases of all studies reporting data on urinary quinolinic acid in human subjects from December 1949 to January 2022. Results Fifty-seven articles met the inclusion criteria. In most of the reported studies, compared to the control group, quinolinic acid was shown to be at increased concentration in urine of patients suffering from different diseases and conditions. This metabolite was also demonstrated to correlate with the severity of certain diseases including juvenile idiopathic inflammatory myopathies, graft vs. host disease, autism spectrum disorder, and prostate cancer. In critically ill patients, elevated quinolinic acid in urine predicted a spectrum of adverse outcomes including hospital mortality. Conclusion Quinolinic acid has been implicated in the pathophysiology of multiple conditions. Its urinary accumulation appears to be a feature of acute physiological stress and several chronic diseases. The exact significance of these findings is still under investigation, and further studies are needed to reveal the subsequent implications of this accumulation.
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Affiliation(s)
- Marie Christelle Saade
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, TX, United States
| | - Amanda J. Clark
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, TX, United States
- Division of Pediatric Nephrology, Department of Pediatrics, University of Texas Southwestern, Dallas, TX, United States
| | - Samir M. Parikh
- Division of Nephrology, Department of Medicine, University of Texas Southwestern, Dallas, TX, United States
- Department of Pharmacology, University of Texas Southwestern, Dallas, TX, United States
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7
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Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022; 414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although metabolomics, alone or combined with other omics data, has already demonstrated its relevance for patient stratification in the frame of research projects and clinical studies, much remains to be done to move this approach to the clinical practice. This is especially true in the perspective of being applied to personalized/precision medicine, which aims at stratifying patients according to their risk of developing diseases, and tailoring medical treatments of patients according to individual characteristics in order to improve their efficacy and limit their toxicity. In this review article, we discuss the main challenges linked to analytical chemistry that need to be addressed to foster the implementation of metabolomics in the clinics and the use of the data produced by this approach in personalized medicine. First of all, there are already well-known issues related to untargeted metabolomics workflows at the levels of data production (lack of standardization), metabolite identification (small proportion of annotated features and identified metabolites), and data processing (from automatic detection of features to multi-omic data integration) that hamper the inter-operability and reusability of metabolomics data. Furthermore, the outputs of metabolomics workflows are complex molecular signatures of few tens of metabolites, often with small abundance variations, and obtained with expensive laboratory equipment. It is thus necessary to simplify these molecular signatures so that they can be produced and used in the field. This last point, which is still poorly addressed by the metabolomics community, may be crucial in a near future with the increased availability of molecular signatures of medical relevance and the increased societal demand for participatory medicine.
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Affiliation(s)
- Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Giulio Rosati
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Christian Moguet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Celia Fuentes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jose Marrugo-Ramírez
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Thibaud Lefebvre
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- Centre de Recherche sur l'Inflammation/CRI, Université de Paris, Inserm, Paris, France
- CRMR Porphyrie, Hôpital Louis Mourier, AP-HP Nord - Université de Paris, Colombes, France
| | - Hervé Volland
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France.
- MetaboHUB, Gif-sur-Yvette, France.
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8
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Meister I, Zhang P, Sinha A, Sköld CM, Wheelock ÅM, Izumi T, Chaleckis R, Wheelock CE. High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem 2021; 93:5248-5258. [PMID: 33739820 PMCID: PMC8041248 DOI: 10.1021/acs.analchem.1c00203] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/26/2021] [Indexed: 12/15/2022]
Abstract
Urine is a noninvasive biofluid that is rich in polar metabolites and well suited for metabolomic epidemiology. However, because of individual variability in health and hydration status, the physiological concentration of urine can differ >15-fold, which can pose major challenges in untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics. Although numerous urine normalization methods have been implemented (e.g., creatinine, specific gravity-SG), most are manual and, therefore, not practical for population-based studies. To address this issue, we developed a method to measure SG in 96-well-plates using a refractive index detector (RID), which exhibited accuracy within 85-115% and <3.4% precision. Bland-Altman statistics showed a mean deviation of -0.0001 SG units (limits of agreement: -0.0014 to 0.0011) relative to a hand-held refractometer. Using this RID-based SG normalization, we developed an automated LC-MS workflow for untargeted urinary metabolomics in a 96-well-plate format. The workflow uses positive and negative ionization HILIC chromatography and acquires mass spectra in data-independent acquisition (DIA) mode at three collision energies. Five technical internal standards (tISs) were used to monitor data quality in each method, all of which demonstrated raw coefficients of variation (CVs) < 10% in the quality controls (QCs) and < 20% in the samples for a small cohort (n = 87 urine samples, n = 22 QCs). Application in a large cohort (n = 842 urine samples, n = 248 QCs) demonstrated CVQC < 5% and CVsamples < 16% for 4/5 tISs after signal drift correction by cubic spline regression. The workflow identified >540 urinary metabolites including endogenous and exogenous compounds. This platform is suitable for performing urinary untargeted metabolomic epidemiology and will be useful for applications in population-based molecular phenotyping.
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Affiliation(s)
- Isabel Meister
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
| | - Pei Zhang
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
| | - Anirban Sinha
- Department
of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
- Department
of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
- Computational
Physiology and Biostatistics, University
Children’s Hospital, Spitalstrasse 33, Basel 4056, Switzerland
| | - C. Magnus Sköld
- Respiratory
Medicine Unit, K2 Department of Medicine Solna and Center for Molecular
Medicine, Karolinska Institutet, Stockholm 141-86, Sweden
- Department
of Respiratory Medicine and Allergy, Karolinska
University Hospital, Stockholm 141-86, Sweden
| | - Åsa M. Wheelock
- Respiratory
Medicine Unit, K2 Department of Medicine Solna and Center for Molecular
Medicine, Karolinska Institutet, Stockholm 141-86, Sweden
- Department
of Respiratory Medicine and Allergy, Karolinska
University Hospital, Stockholm 141-86, Sweden
| | - Takashi Izumi
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Department
of Biochemistry, Gunma University Graduate
School of Medicine, 3-39-22
Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Romanas Chaleckis
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
| | - Craig E. Wheelock
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
- Department
of Respiratory Medicine and Allergy, Karolinska
University Hospital, Stockholm 141-86, Sweden
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