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Datta I, Zahoor I, Ata N, Rashid F, Cerghet M, Rattan R, Poisson LM, Giri S. Utility of an Untargeted Metabolomics Approach Using a 2D GC-GC-MS Platform to Distinguish Relapsing and Progressive Multiple Sclerosis. Metabolites 2024; 14:493. [PMID: 39330500 DOI: 10.3390/metabo14090493] [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: 07/13/2024] [Revised: 08/19/2024] [Accepted: 08/28/2024] [Indexed: 09/28/2024] Open
Abstract
Multiple sclerosis (MS) is the most common inflammatory neurodegenerative disease of the central nervous system (CNS) in young adults and results in progressive neurological defects. The relapsing-remitting phenotype (RRMS) is the most common disease course in MS, which ultimately progresses to secondary progressive MS (SPMS), while primary progressive MS (PPMS) is a type of MS that worsens gradually over time without remissions. There is a gap in knowledge regarding whether the relapsing form can be distinguished from the progressive course, or healthy subjects (HS) based on an altered serum metabolite profile. In this study, we performed global untargeted metabolomics with the 2D GC-GC-MS platform to identify altered metabolites between RRMS, PPMS, and HS. We profiled 235 metabolites in the serum of patients with RRMS (n = 41), PPMS (n = 31), and HS (n = 91). A comparison of RRMS and HS patients revealed 22 significantly altered metabolites at p < 0.05 (false-discovery rate [FDR] = 0.3). The PPMS and HS comparisons revealed 28 altered metabolites at p < 0.05 (FDR = 0.2). Pathway analysis using MetaboAnalyst revealed enrichment of four metabolic pathways in both RRMS and PPMS (hypergeometric test p < 0.05): (1) galactose metabolism; (2) amino sugar and nucleotide sugar metabolism; (3) phenylalanine, tyrosine, and tryptophan biosynthesis; and (4) aminoacyl-tRNA biosynthesis. The Qiagen IPA enrichment test identified the sulfatase 2 (SULF2) (p = 0.0033) and integrin subunit beta 1 binding protein 1 (ITGB1BP1) (p = 0.0067) genes as upstream regulators of altered metabolites in the RRMS vs. HS groups. However, in the PPMS vs. HS comparison, valine was enriched in the neurodegeneration of brain cells (p = 0.05), and heptadecanoic acid, alpha-ketoisocaproic acid, and glycerol participated in inflammation in the CNS (p = 0.03). Overall, our study suggests that RRMS and PPMS may contribute metabolic fingerprints in the form of unique altered metabolites for discriminating MS disease from HS, with the potential for constructing a metabolite panel for progressive autoimmune diseases such as MS.
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Affiliation(s)
- Indrani Datta
- Department of Public Health Sciences, Henry Ford Health, Detroit, MI 48202, USA
- Department of Neurosurgery, Henry Ford Health, Detroit, MI 48202, USA
| | - Insha Zahoor
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Nasar Ata
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Faraz Rashid
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Mirela Cerghet
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
| | - Ramandeep Rattan
- Women's Health Services, Henry Ford Health, Detroit, MI 48202, USA
| | - Laila M Poisson
- Department of Public Health Sciences, Henry Ford Health, Detroit, MI 48202, USA
| | - Shailendra Giri
- Department of Neurology, Henry Ford Health, Detroit, MI 48202, USA
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Montis A, Delporte C, Noda Y, Stoffelen P, Stévigny C, Hermans C, Van Antwerpen P, Souard F. Targeted metabolomics and transcript profiling of methyltransferases in three coffee species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112117. [PMID: 38750798 DOI: 10.1016/j.plantsci.2024.112117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/08/2024] [Accepted: 05/11/2024] [Indexed: 05/23/2024]
Abstract
Coffee plants contain well-known xanthines as caffeine. Three Coffea species grown in a controlled greenhouse environment were the focus of this research. Coffea arabica and C. canephora are two first principal commercial species and commonly known as arabica and robusta, respectively. Originating in Central Africa, C. anthonyi is a novel species with small leaves. The xanthine metabolites in flower, fruit and leaf extracts were compared using both targeted and untargeted metabolomics approaches. We evaluated how the xanthine derivatives and FQA isomers relate to the expression of biosynthetic genes encoding N- and O-methyltransferases. Theobromine built up in leaves of C. anthonyi because caffeine biosynthesis was hindered in the absence of synthase gene expression. Despite this, green fruits expressed these genes and they produced caffeine. Given that C. anthonyi evolved successfully over time, these findings put into question the defensive role of caffeine in leaves. An overview of the histolocalisation of xanthines in the different flower parts of Coffea arabica was also provided. The gynoecium contained more theobromine than the flower buds or petals. This could be attributed to increased caffeine biosynthesis before fructification. The presence of theophylline and the absence of theobromine in the petals indicate that caffeine is catabolized more in the petals than in the gynoecium.
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Affiliation(s)
- Andrea Montis
- RD3 Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/05, Brussels 1050, Belgium; APFP Analytical platform of the Faculty of Pharmacy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/5, Brussels 1050, Belgium
| | - Cédric Delporte
- RD3 Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/05, Brussels 1050, Belgium; APFP Analytical platform of the Faculty of Pharmacy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/5, Brussels 1050, Belgium
| | - Yusaku Noda
- The National Institutes for Quantum Science and Technology (QST), Takasaki Institute for Advanced Quantum Science, Gunma, 370-1292, Japan
| | - Piet Stoffelen
- Meise Botanic Garden, Domein van Bouchout, Nieuwe laan 38, Meise 1860, Belgium
| | - Caroline Stévigny
- RD3 Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/05, Brussels 1050, Belgium
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Brussels Bioengineering School, Université libre de Bruxelles, Campus Plaine, CP 245, Brussels 1050, Belgium
| | - Pierre Van Antwerpen
- RD3 Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/05, Brussels 1050, Belgium; APFP Analytical platform of the Faculty of Pharmacy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/5, Brussels 1050, Belgium.
| | - Florence Souard
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes, 470 rue de la chimie, Saint-Martin d'Hères 38400, France; DPP Department - Unit of Pharmacology, Pharmacotherapy and Pharmaceutical care, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/07, Brussels 1050, Belgium
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He S, Zhu G, Zhou Y, Yang B, Wang J, Wang Z, Wang T. Predictive models for personalized precision medical intervention in spontaneous regression stages of cervical precancerous lesions. J Transl Med 2024; 22:686. [PMID: 39061062 PMCID: PMC11282852 DOI: 10.1186/s12967-024-05417-y] [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: 01/24/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND During the prolonged period from Human Papillomavirus (HPV) infection to cervical cancer development, Low-Grade Squamous Intraepithelial Lesion (LSIL) stage provides a critical opportunity for cervical cancer prevention, giving the high potential for reversal in this stage. However, there is few research and a lack of clear guidelines on appropriate intervention strategies at this stage, underscoring the need for real-time prognostic predictions and personalized treatments to promote lesion reversal. METHODS We have established a prospective cohort. Since 2018, we have been collecting clinical data and pathological images of HPV-infected patients, followed by tracking the progression of their cervical lesions. In constructing our predictive models, we applied logistic regression and six machine learning models, evaluating each model's predictive performance using metrics such as the Area Under the Curve (AUC). We also employed the SHAP method for interpretative analysis of the prediction results. Additionally, the model identifies key factors influencing the progression of the lesions. RESULTS Model comparisons highlighted the superior performance of Random Forests (RF) and Support Vector Machines (SVM), both in clinical parameter and pathological image-based predictions. Notably, the RF model, which integrates pathological images and clinical multi-parameters, achieved the highest AUC of 0.866. Another significant finding was the substantial impact of sleep quality on the spontaneous clearance of HPV and regression of LSIL. CONCLUSIONS In contrast to current cervical cancer prediction models, our model's prognostic capabilities extend to the spontaneous regression stage of cervical cancer. This model aids clinicians in real-time monitoring of lesions and in developing personalized treatment or follow-up plans by assessing individual risk factors, thus fostering lesion spontaneous reversal and aiding in cervical cancer prevention and reduction.
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Affiliation(s)
- Simin He
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Ministry of Education, Taiyuan, 030001, China
| | - Guiming Zhu
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Ministry of Education, Taiyuan, 030001, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Boran Yang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Ministry of Education, Taiyuan, 030001, China
| | - Juping Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Ministry of Education, Taiyuan, 030001, China
| | - Zhaoxia Wang
- Department of Obstetrics and Gynecology, First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Tong Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China.
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Ministry of Education, Taiyuan, 030001, China.
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Sun D, Chasseur C, Mathieu F, Lechanteur J, Van Antwerpen P, Rasschaert J, Fontaine V, Delporte C. Untargeted Metabolomics Approach Correlated Enniatin B Mycotoxin Presence in Cereals with Kashin-Beck Disease Endemic Regions of China. Toxins (Basel) 2023; 15:533. [PMID: 37755959 PMCID: PMC10537395 DOI: 10.3390/toxins15090533] [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] [Received: 06/25/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
Kashin-Beck disease (KBD) is a multifactorial endemic disease that only occurs in specific Asian areas. Mycotoxin contamination, especially from the Fusarium spp., has been considered as one of the environmental risk factors that could provoke chondrocyte and cartilage damage. This study aimed to investigate whether new mycotoxins could be identified in KBD-endemic regions as a potential KBD risk factor. This was investigated on 292 barley samples collected in Tibet during 2009-2016 and 19 wheat samples collected in Inner Mongolia in 2006, as control, from KBD-endemic and non-endemic areas. The LC-HRMS(/MS) data, obtained by a general mycotoxin extraction technic, were interpreted by both untargeted metabolomics and molecular networks, allowing us to identify a discriminating compound, enniatin B, a mycotoxin produced by some Fusarium spp. The presence of Fusarium spp. DNA was detected in KBD-endemic area barley samples. Further studies are required to investigate the role of this mycotoxin in KBD development in vivo.
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Affiliation(s)
- Danlei Sun
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium (V.F.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery Unit & Analytical Platform of the Faculty of Pharmacy (APFP), Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium;
| | - Camille Chasseur
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium (V.F.)
| | | | - Jessica Lechanteur
- Laboratory of Bone and Metabolic Biochemistry, Faculty of Medicine, Université libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.L.); (J.R.)
| | - Pierre Van Antwerpen
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery Unit & Analytical Platform of the Faculty of Pharmacy (APFP), Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium;
| | - Joanne Rasschaert
- Laboratory of Bone and Metabolic Biochemistry, Faculty of Medicine, Université libre de Bruxelles (ULB), 1070 Brussels, Belgium; (J.L.); (J.R.)
| | - Véronique Fontaine
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium (V.F.)
| | - Cédric Delporte
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery Unit & Analytical Platform of the Faculty of Pharmacy (APFP), Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium;
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Bergeat D, Coquery N, Gautier Y, Clotaire S, Vincent É, Romé V, Guérin S, Le Huërou-Luron I, Blat S, Thibault R, Val-Laillet D. Exploration of fMRI brain responses to oral sucrose after Roux-en-Y gastric bypass in obese yucatan minipigs in relationship with microbiota and metabolomics profiles. Clin Nutr 2023; 42:394-410. [PMID: 36773369 DOI: 10.1016/j.clnu.2023.01.015] [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] [Received: 07/26/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND & AIMS In most cases, Roux-en-Y gastric bypass (RYGBP) is an efficient intervention to lose weight, change eating behavior and improve metabolic outcomes in obese patients. We hypothesized that weight loss induced by RYGBP in obese Yucatan minipigs would induce specific modifications of the gut-brain axis and neurocognitive responses to oral sucrose stimulation in relationship with food intake control. METHODS An integrative study was performed after SHAM (n = 8) or RYGBP (n = 8) surgery to disentangle the physiological, metabolic and neurocognitive mechanisms of RYGBP. BOLD fMRI responses to sucrose stimulations at different concentrations, brain mRNA expression, cecal microbiota, and plasma metabolomics were explored 4 months after surgery and integrated with WGCNA analysis. RESULTS We showed that weight loss induced by RYGBP or SHAM modulated differently the frontostriatal responses to oral sucrose stimulation, suggesting a different hedonic treatment and inhibitory control related to palatable food after RYGBP. The expression of brain genes involved in the serotoninergic and cannabinoid systems were impacted by RYGBP. Cecal microbiota was deeply modified and many metabolite features were differentially increased in RYGBP. Data integration with WGCNA identified interactions between key drivers of OTUs and metabolites features linked to RYGBP. CONCLUSION This longitudinal study in the obese minipig model illustrates with a systemic and integrative analysis the mid-term consequences of RYGBP on brain mRNA expression, cecal microbiota and plasma metabolites. We confirmed the impact of RYGBP on functional brain responses related to food reward, hedonic evaluation and inhibitory control, which are key factors for the success of anti-obesity therapy and weight loss maintenance.
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Affiliation(s)
- Damien Bergeat
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France; Department of Digestive Surgery, CHU Rennes, Rennes, France
| | - Nicolas Coquery
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Yentl Gautier
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Sarah Clotaire
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Émilie Vincent
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Véronique Romé
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Sylvie Guérin
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Isabelle Le Huërou-Luron
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Sophie Blat
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France
| | - Ronan Thibault
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France; Department of Endocrinology-Diabetology-Nutrition, Home Parenteral Nutrition Centre, CHU Rennes, Rennes, France.
| | - David Val-Laillet
- Inrae, Inserm, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, St Gilles, France.
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GeneSelectML: a comprehensive way of gene selection for RNA-Seq data via machine learning algorithms. Med Biol Eng Comput 2023; 61:229-241. [PMID: 36355333 DOI: 10.1007/s11517-022-02695-w] [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: 10/23/2021] [Accepted: 10/02/2022] [Indexed: 11/11/2022]
Abstract
Selection of differentially expressed genes (DEGs) is a vital process to discover the causes of diseases. It has been shown that modelling of genomics data by considering relation among genes increases the predictive performance of methods compared to univariate analysis. However, there exist serious differences among most studies analyzing the same dataset for the reasons arising from the methods. Therefore, there is a strong need for easily accessible, user-friendly, and interactive tool to perform gene selection for RNA-seq data via machine learning algorithms simultaneously not to miss DEGs. We develop an open-source and freely available web-based tool for gene selection via machine learning algorithms that can deal with high performance computation. This tool includes six machine learning algorithms having different aspects. Moreover, the tool involves classical pre-processing steps; filtering, normalization, transformation, and univariate analysis. It also offers well-arranged graphical approaches; network plot, heatmap, venn diagram, and box-and-whisker plot. Gene ontology analysis is provided for both mRNA and miRNA DEGs. The implementation is carried out on Alzheimer RNA-seq data to demonstrate the use of this web-based tool. Eleven genes are suggested by at least two out of six methods. One of these genes, hsa-miR-148a-3p, might be considered as a new biomarker for Alzheimer's disease diagnosis. Kidney Chromophobe dataset is also analyzed to demonstrate the validity of GeneSelectML web tool on a different dataset. GeneSelectML is distinguished in that it simultaneously uses different machine learning algorithms for gene selection and can perform pre-processing, graphical representation, and gene ontology analyses on the same tool. This tool is freely available at www.softmed.hacettepe.edu.tr/GeneSelectML .
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Dinis K, Tsamba L, Thomas F, Jamin E, Camel V. Preliminary authentication of apple juices using untargeted UHPLC-HRMS analysis combined to chemometrics. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Targeted and Untargeted Mass Spectrometry-Based Metabolomics for Chemical Profiling of Three Coffee Species. Molecules 2022; 27:molecules27103152. [PMID: 35630628 PMCID: PMC9143251 DOI: 10.3390/molecules27103152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022] Open
Abstract
While coffee beans have been studied for many years, researchers are showing a growing interest in coffee leaves and by-products, but little information is currently available on coffee species other than Coffea arabica and Coffea canephora. The aim of this work was to perform a targeted and untargeted metabolomics study on Coffea arabica, Coffea canephora and Coffea anthonyi. The application of the recent high-resolution mass spectrometry-based metabolomics tools allowed us to gain a clear overview of the main differences among the coffee species. The results showed that the leaves and fruits of Coffea anthonyi had a different metabolite profile when compared to the two other species. In Coffea anthonyi, caffeine levels were found in lower concentrations while caffeoylquinic acid and mangiferin-related compounds were found in higher concentrations. A large number of specialized metabolites can be found in Coffea anthonyi tissues, making this species a valid candidate for innovative healthcare products made with coffee extracts.
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Colas L, Royer AL, Massias J, Raux A, Chesneau M, Kerleau C, Guerif P, Giral M, Guitton Y, Brouard S. Urinary metabolomic profiling from spontaneous tolerant kidney transplanted recipients shows enrichment in tryptophan-derived metabolites. EBioMedicine 2022; 77:103844. [PMID: 35241402 PMCID: PMC9034456 DOI: 10.1016/j.ebiom.2022.103844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/27/2022] Open
Abstract
Background Operational tolerance is the holy grail in solid organ transplantation. Previous reports showed that the urinary compartment of operationally tolerant recipients harbor a specific and unique profile. We hypothesized that spontaneous tolerant kidney transplanted recipients (KTR) would have a specific urinary metabolomic profile associated to operational tolerance. Methods We performed metabolomic profiling on urine samples from healthy volunteers, stable KTR under standard and minimal immunosuppression and spontaneous tolerant KTR using liquid chromatography in tandem with mass spectrometry. Supervised and unsupervised multivariate computational analyses were used to highlight urinary metabolomic profile and metabolite identification thanks to workflow4metabolomic platform. Findings The urinary metabolome was composed of approximately 2700 metabolites. Raw unsupervised clustering allowed us to separate healthy volunteers and tolerant KTR from others. We confirmed by two methods a specific urinary metabolomic signature in tolerant KTR mainly driven by kynurenic acid independent of immunosuppressive drugs, serum creatinine and gender. Interpretation Kynurenic acid and tryptamine enrichment allowed the identification of putative pathways and metabolites associated with operational tolerance like IDO, GRP35 and AhR and indole alkaloids. Funding This study was supported by the ANR, IRSRPL and CHU de Nantes.
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Affiliation(s)
- Luc Colas
- CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Centre Hospitalier, Nantes Université, 30 bd Jean Monnet, Nantes F-44000, France.
| | - Anne-Lise Royer
- MELISA Core Facility, Oniris, INRΑE, Nantes F-44307, France; Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAE, Nantes F-44307, France.
| | - Justine Massias
- MELISA Core Facility, Oniris, INRΑE, Nantes F-44307, France; Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAE, Nantes F-44307, France.
| | - Axel Raux
- MELISA Core Facility, Oniris, INRΑE, Nantes F-44307, France; Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAE, Nantes F-44307, France.
| | - Mélanie Chesneau
- CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Centre Hospitalier, Nantes Université, 30 bd Jean Monnet, Nantes F-44000, France.
| | - Clarisse Kerleau
- CHU Nantes, Service de Néphrologie-Immunologie Clinique, Nantes Université, Nantes, France.
| | - Pierrick Guerif
- CHU Nantes, Service de Néphrologie-Immunologie Clinique, Nantes Université, Nantes, France.
| | - Magali Giral
- CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Centre Hospitalier, Nantes Université, 30 bd Jean Monnet, Nantes F-44000, France; CHU Nantes, Service de Néphrologie-Immunologie Clinique, Nantes Université, Nantes, France; Centre d'Investigation Clinique en Biothérapie, Centre de Ressources Biologiques (CRB), Nantes, France.
| | - Yann Guitton
- MELISA Core Facility, Oniris, INRΑE, Nantes F-44307, France; Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAE, Nantes F-44307, France.
| | - Sophie Brouard
- CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Centre Hospitalier, Nantes Université, 30 bd Jean Monnet, Nantes F-44000, France; CHU Nantes, Service de Néphrologie-Immunologie Clinique, Nantes Université, Nantes, France; Labex IGO, Nantes, France.
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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: 35] [Impact Index Per Article: 17.5] [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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11
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Imbert A, Rompais M, Selloum M, Castelli F, Mouton-Barbosa E, Brandolini-Bunlon M, Chu-Van E, Joly C, Hirschler A, Roger P, Burger T, Leblanc S, Sorg T, Ouzia S, Vandenbrouck Y, Médigue C, Junot C, Ferro M, Pujos-Guillot E, de Peredo AG, Fenaille F, Carapito C, Herault Y, Thévenot EA. ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. Sci Data 2021; 8:311. [PMID: 34862403 PMCID: PMC8642540 DOI: 10.1038/s41597-021-01095-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/02/2021] [Indexed: 01/20/2023] Open
Abstract
Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the Lat (linker for activation of T cells) and the Mx2 (MX dynamin-like GTPase 2) genes, respectively. Our dataset consists of 9 assays (1 preclinical, 2 proteomics and 6 metabolomics) generated with a fully non-targeted and standardized approach. The data and processing code are publicly available in the ProMetIS R package to ensure accessibility, interoperability, and reusability. The dataset thus provides unique molecular information about the physiological role of the Lat and Mx2 genes. Furthermore, the protocols described herein can be easily extended to a larger number of individuals and tissues. Finally, this resource will be of great interest to develop new bioinformatic and biostatistic methods for multi-omics data integration.
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Affiliation(s)
- Alyssa Imbert
- CEA, LIST, Laboratoire Sciences des Données et de la Décision, IFB, MetaboHUB, Gif-sur-Yvette, France.
- IFB-core, UMS3601, Genoscope, Evry, France.
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, ProFI, Strasbourg, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
| | - Florence Castelli
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, ProFI, Toulouse, France
| | - Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB, Clermont-Ferrand, France
| | - Emeline Chu-Van
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB, Clermont-Ferrand, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, ProFI, Strasbourg, France
| | - Pierrick Roger
- CEA, LIST, Laboratoire Intelligence Artificielle et Apprentissage Automatique, MetaboHUB, Gif-sur-Yvette, France
| | - Thomas Burger
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, FR2048, ProFI, Grenoble, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
| | - Sadia Ouzia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Yves Vandenbrouck
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, FR2048, ProFI, Grenoble, France
| | - Claudine Médigue
- IFB-core, UMS3601, Genoscope, Evry, France
- Laboratoire d'Analyses Bioinformatique en Génomique et Métabolisme (LABGeM), CNRS & CEA/DRF/IFJ, UMR8030, Evry, France
| | - Christophe Junot
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Myriam Ferro
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, FR2048, ProFI, Grenoble, France
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB, Clermont-Ferrand, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, ProFI, Toulouse, France
| | - François Fenaille
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, ProFI, Strasbourg, France
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
| | - Etienne A Thévenot
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France.
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12
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Tinel C, Lamarthée B, Callemeyn J, Van Loon E, Sauvaget V, Morin L, Aouni L, Rabant M, Gwinner W, Marquet P, Naesens M, Anglicheau D. Integrative Omics Analysis Unravels Microvascular Inflammation-Related Pathways in Kidney Allograft Biopsies. Front Immunol 2021; 12:738795. [PMID: 34795664 PMCID: PMC8593247 DOI: 10.3389/fimmu.2021.738795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/15/2021] [Indexed: 12/29/2022] Open
Abstract
In solid-organ transplantation, microRNAs (miRNAs) have emerged as key players in the regulation of allograft cells function in response to injury. To gain insight into the role of miRNAs in antibody-mediated rejection, a rejection phenotype histologically defined by microvascular inflammation, kidney allograft biopsies were subjected to miRNA but also messenger RNA (mRNA) profiling. Using a unique multistep selection process specific to the BIOMARGIN study (discovery cohort, N=86; selection cohort, N=99; validation cohort, N=298), six differentially expressed miRNAs were consistently identified: miR-139-5p (down) and miR-142-3p/150-5p/155-5p/222-3p/223-3p (up). Their expression level gradually correlated with microvascular inflammation intensity. The cell specificity of miRNAs target genes was investigated by integrating their in vivo mRNA targets with single-cell RNA sequencing from an independent allograft biopsy cohort. Endothelial-derived miR-139-5p expression correlated negatively with MHC-related genes expression. Conversely, epithelial-derived miR-222-3p overexpression was strongly associated with degraded renal electrolyte homeostasis and repressed immune-related pathways. In immune cells, miR-150-5p regulated NF-κB activation in T lymphocytes whereas miR-155-5p regulated mRNA splicing in antigen-presenting cells. Altogether, integrated omics enabled us to unravel new pathways involved in microvascular inflammation and suggests that metabolism modifications in tubular epithelial cells occur as a consequence of antibody-mediated rejection, beyond the nearby endothelial compartment.
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Affiliation(s)
- Claire Tinel
- Necker-Enfants Malades Institute, Institut national de la santé et de la recherche médicale (Inserm) U1151, Université de Paris, Paris, France
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Baptiste Lamarthée
- Necker-Enfants Malades Institute, Institut national de la santé et de la recherche médicale (Inserm) U1151, Université de Paris, Paris, France
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Virginia Sauvaget
- Necker-Enfants Malades Institute, Institut national de la santé et de la recherche médicale (Inserm) U1151, Université de Paris, Paris, France
| | - Lise Morin
- Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laïla Aouni
- Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Marion Rabant
- Necker-Enfants Malades Institute, Institut national de la santé et de la recherche médicale (Inserm) U1151, Université de Paris, Paris, France
- Department of Pathology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Pierre Marquet
- Institut national de la santé et de la recherche médicale (Inserm), University of Limoges, Limoges University Hospital, Pharmacology & Transplantation, Limoges, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Dany Anglicheau
- Necker-Enfants Malades Institute, Institut national de la santé et de la recherche médicale (Inserm) U1151, Université de Paris, Paris, France
- Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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13
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FlowCT for the analysis of large immunophenotypic datasets and biomarker discovery in cancer immunology. Blood Adv 2021; 6:690-703. [PMID: 34587246 PMCID: PMC8791585 DOI: 10.1182/bloodadvances.2021005198] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Large-scale immune monitoring is becoming routinely used in clinical trials to identify determinants of treatment responsiveness, particularly to immunotherapies. Flow cytometry remains one of the most versatile and high throughput approaches for single-cell analysis; however, manual interpretation of multidimensional data poses a challenge to capture full cellular diversity and provide reproducible results. We present FlowCT, a semi-automated workspace empowered to analyze large datasets that includes pre-processing, normalization, multiple dimensionality reduction techniques, automated clustering and predictive modeling tools. As a proof of concept, we used FlowCT to compare the T cell compartment in bone marrow (BM) vs peripheral blood (PB) of patients with smoldering multiple myeloma (MM); identify minimally-invasive immune biomarkers of progression from smoldering to active MM; define prognostic T cell subsets in the BM of patients with active MM after treatment intensification; and assess the longitudinal effect of maintenance therapy in BM T cells. A total of 354 samples were analyzed and immune signatures predictive of malignant transformation in 150 smoldering MM patients (hazard ratio [HR]: 1.7; P <.001), and of progression-free (HR: 4.09; P <.0001) and overall survival (HR: 3.12; P =.047) in 100 active MM patients, were identified. New data also emerged about stem cell memory T cells, the concordance between immune profiles in BM vs PB and the immunomodulatory effect of maintenance therapy. FlowCT is a new open-source computational approach that can be readily implemented by research laboratories to perform quality-control, analyze high-dimensional data, unveil cellular diversity and objectively identify biomarkers in large immune monitoring studies.
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14
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Rojo-Poveda O, Ribeiro SO, Anton-Sales C, Keymeulen F, Barbosa-Pereira L, Delporte C, Zeppa G, Stévigny C. Evaluation of Cocoa Bean Shell Antimicrobial Activity: A Tentative Assay Using a Metabolomic Approach for Active Compound Identification. PLANTA MEDICA 2021; 87:841-849. [PMID: 34020491 DOI: 10.1055/a-1499-7829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cocoa bean shell is one of the main by-products of chocolate manufacturing and possesses several compounds with biofunctionalities. It can function as an antibacterial agent, and its action is mostly reported against Streptococcus mutans. However, only a few studies have investigated the cocoa bean shell compounds responsible for this activity. This study aimed to evaluate several extracts of cocoa bean shells from different geographical origins and cocoa varieties and estimate their antimicrobial properties against different fungal and bacterial strains by determining their minimal inhibitory concentration. The results demonstrated antimicrobial activity of cocoa bean shell against one of the tested strains, S. mutans. Cocoa bean shell extracts were further analysed via LC-HRMS for untargeted metabolomic analysis. LC-HRMS data were analysed (preprocessing and statistical analyses) using the Workflow4Metabolomics platform. The latter enabled us to identify possible compounds responsible for the detected antimicrobial activity by comparing the more and less active extracts. Active extracts were not the most abundant in polyphenols but contained higher concentrations of two metabolites. After tentative annotation of these metabolites, one of them was identified and confirmed to be 7-methylxanthine. When tested alone, 7-methylxanthine did not display antibacterial activity. However, a possible cocktail effect due to the synergistic activity of this molecule along with other compounds in the cocoa bean shell extracts cannot be neglected. In conclusion, cocoa bean shell could be a functional ingredient with benefits for human health as it exhibited antibacterial activity against S. mutans. However, the antimicrobial mechanisms still need to be confirmed.
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Affiliation(s)
- Olga Rojo-Poveda
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
- Department of Agriculture, Forestry and Food Sciences (DISAFA), University of Turin, Grugliasco, Italy
| | - Sofia Oliveira Ribeiro
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Cèlia Anton-Sales
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Flore Keymeulen
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Letricia Barbosa-Pereira
- Department of Agriculture, Forestry and Food Sciences (DISAFA), University of Turin, Grugliasco, Italy
- Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Cédric Delporte
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
- Analytical Platform of the Faculty of Pharmacy (APFP), Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Giuseppe Zeppa
- Department of Agriculture, Forestry and Food Sciences (DISAFA), University of Turin, Grugliasco, Italy
| | - Caroline Stévigny
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
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15
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Vanhaverbeke C, Touboul D, Elie N, Prévost M, Meunier C, Michelland S, Cunin V, Ma L, Vermijlen D, Delporte C, Pochet S, Le Gouellec A, Sève M, Van Antwerpen P, Souard F. Untargeted metabolomics approach to discriminate mistletoe commercial products. Sci Rep 2021; 11:14205. [PMID: 34244531 PMCID: PMC8270909 DOI: 10.1038/s41598-021-93255-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/17/2021] [Indexed: 01/25/2023] Open
Abstract
Mistletoe (Viscum album L.) is used in German-speaking European countries in the field of integrative oncology linking conventional and complementary medicine therapies to improve quality of life. Various companies sell extracts, fermented or not, for injection by subcutaneous or intra-tumoral route with a regulatory status of anthroposophic medicinal products (European Medicinal Agency (EMA) assessment status). These companies as well as anthroposophical physicians argue that complex matrices composed of many molecules in mixture are necessary for activity and that the host tree of the mistletoe parasitic plant is the main determining factor for this matrix composition. The critical point is that parenteral devices of European mistletoe extracts do not have a standard chemical composition regulated by EMA quality guidelines, because they are not drugs, regulatory speaking. However, the mechanism of mistletoe's anticancer activity and its effectiveness in treating and supporting cancer patients are not fully understood. Because of this lack of transparency and knowledge regarding the matrix chemical composition, we undertook an untargeted metabolomics study of several mistletoe extracts to explore and compare their fingerprints by LC-(HR)MS(/MS) and 1H-NMR. Unexpectedly, we showed that the composition was primarily driven by the manufacturer/preparation method rather than the different host trees. This differential composition may cause differences in immunostimulating and anti-cancer activities of the different commercially available mistletoe extracts as illustrated by structure-activity relationships based on LC-MS/MS and 1H-NMR identifications completed by docking experiments. In conclusion, in order to move towards an evidence-based medicine use of mistletoe, it is a priority to bring rigor and quality, chemically speaking.
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Affiliation(s)
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Nicolas Elie
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Cécile Meunier
- CHU Grenoble Alpes, Service de Biochimie et Biologie moléculaire et Toxicologie Environnementale, 38000, Grenoble, France
| | - Sylvie Michelland
- Univ. Grenoble Alpes, CHU Grenoble Alpes, Plateforme GExiM, 38000, Grenoble, France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Valérie Cunin
- Univ. Grenoble Alpes, CHU Grenoble Alpes, Plateforme GExiM, 38000, Grenoble, France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Ling Ma
- Department of Pharmacotherapy and Pharmaceutics (DPP), Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
- Institute for Medical Immunology, Université libre de Bruxelles, 6041, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Université libre de Bruxelles (ULB), Brussels, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics (DPP), Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
- Institute for Medical Immunology, Université libre de Bruxelles, 6041, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Delporte
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform of the Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Stéphanie Pochet
- Department of Pharmacotherapy and Pharmaceutics (DPP), Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Audrey Le Gouellec
- CHU Grenoble Alpes, Service de Biochimie et Biologie moléculaire et Toxicologie Environnementale, 38000, Grenoble, France
- Univ. Grenoble Alpes, CHU Grenoble Alpes, Plateforme GExiM, 38000, Grenoble, France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Michel Sève
- Univ. Grenoble Alpes, CHU Grenoble Alpes, Plateforme GExiM, 38000, Grenoble, France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Pierre Van Antwerpen
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform of the Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Florence Souard
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
- Department of Pharmacotherapy and Pharmaceutics (DPP), Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
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16
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Comte B, Monnerie S, Brandolini-Bunlon M, Canlet C, Castelli F, Chu-Van E, Colsch B, Fenaille F, Joly C, Jourdan F, Lenuzza N, Lyan B, Martin JF, Migné C, Morais JA, Pétéra M, Poupin N, Vinson F, Thevenot E, Junot C, Gaudreau P, Pujos-Guillot E. Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men. EBioMedicine 2021; 69:103440. [PMID: 34161887 PMCID: PMC8237302 DOI: 10.1016/j.ebiom.2021.103440] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Metabolic syndrome (MetS), a cluster of factors associated with risks of developing cardiovascular diseases, is a public health concern because of its growing prevalence. Considering the combination of concomitant components, their development and severity, MetS phenotypes are largely heterogeneous, inducing disparity in diagnosis. METHODS A case/control study was designed within the NuAge longitudinal cohort on aging. From a 3-year follow-up of 123 stable individuals, we present a deep phenotyping approach based on a multiplatform metabolomics and lipidomics untargeted strategy to better characterize metabolic perturbations in MetS and define a comprehensive MetS signature stable over time in older men. FINDINGS We characterize significant changes associated with MetS, involving modulations of 476 metabolites and lipids, and representing 16% of the detected serum metabolome/lipidome. These results revealed a systemic alteration of metabolism, involving various metabolic pathways (urea cycle, amino-acid, sphingo- and glycerophospholipid, and sugar metabolisms…) not only intrinsically interrelated, but also reflecting environmental factors (nutrition, microbiota, physical activity…). INTERPRETATION These findings allowed identifying a comprehensive MetS signature, reduced to 26 metabolites for future translation into clinical applications for better diagnosing MetS. FUNDING The NuAge Study was supported by a research grant from the Canadian Institutes of Health Research (CIHR; MOP-62842). The actual NuAge Database and Biobank, containing data and biologic samples of 1,753 NuAge participants (from the initial 1,793 participants), are supported by the Fonds de recherche du Québec (FRQ; 2020-VICO-279753), the Quebec Network for Research on Aging, a thematic network funded by the Fonds de Recherche du Québec - Santé (FRQS) and by the Merck-Frost Chair funded by La Fondation de l'Université de Sherbrooke. All metabolomics and lipidomics analyses were funded and performed within the metaboHUB French infrastructure (ANR-INBS-0010). All authors had full access to the full data in the study and accept responsibility to submit for publication.
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Affiliation(s)
- Blandine Comte
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Stéphanie Monnerie
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Cécile Canlet
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Florence Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Emeline Chu-Van
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Fabien Jourdan
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Natacha Lenuzza
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Bernard Lyan
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Jean-François Martin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Carole Migné
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - José A Morais
- Division de Gériatrie, McGill University, Center de recherche du Center universitaire de santé McGill, Montreal, Canada
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Nathalie Poupin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Florence Vinson
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Etienne Thevenot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Pierrette Gaudreau
- Center de Recherche du Center hospitalier de l'Université de Montréal, Montreal, Canada; Département de médecine, Université de Montréal, Montreal, Canada
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France.
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17
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Marchand J, Guitton Y, Martineau E, Royer AL, Balgoma D, Le Bizec B, Giraudeau P, Dervilly G. Extending the Lipidome Coverage by Combining Different Mass Spectrometric Platforms: An Innovative Strategy to Answer Chemical Food Safety Issues. Foods 2021; 10:foods10061218. [PMID: 34071212 PMCID: PMC8230090 DOI: 10.3390/foods10061218] [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: 03/03/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 01/30/2023] Open
Abstract
From a general public health perspective, a strategy combining non-targeted and targeted lipidomics MS-based approaches is proposed to identify disrupted patterns in serum lipidome upon growth promoter treatment in pigs. Evaluating the relative contributions of the platforms involved, the study aims at investigating the potential of innovative analytical approaches to highlight potential chemical food safety threats. Serum samples collected during an animal experiment involving control and treated pigs, whose food had been supplemented with ractopamine, were extracted and characterised using three MS strategies: Non-targeted RP LC-HRMS; the targeted Lipidyzer™ platform (differential ion mobility associated with shotgun lipidomics) and a homemade LC-HRMS triglyceride platform. The strategy enabled highlighting specific lipid profile patterns involving various lipid classes, mainly in relation to cholesterol esters, sphingomyelins, lactosylceramide, phosphatidylcholines and triglycerides. Thanks to the combination of non-targeted and targeted MS approaches, various compartments of the pig serum lipidome could be explored, including commonly characterised lipids (Lipidyzer™), triglyceride isomers (Triglyceride platform) and unique lipid features (non-targeted LC-HRMS). Thanks to their respective characteristics, the complementarity of the three tools could be demonstrated for public health purposes, with enhanced coverage, level of characterization and applicability.
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Affiliation(s)
- Jérémy Marchand
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
- CEISAM UMR 6230, Université de Nantes, CNRS, 44000 Nantes, France;
| | - Yann Guitton
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - Estelle Martineau
- CEISAM UMR 6230, Université de Nantes, CNRS, 44000 Nantes, France;
- SpectroMaîtrise, CAPACITES SAS, 26 Bd Vincent Gâche, 44200 Nantes, France
| | - Anne-Lise Royer
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - David Balgoma
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - Bruno Le Bizec
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - Patrick Giraudeau
- CEISAM UMR 6230, Université de Nantes, CNRS, 44000 Nantes, France;
- Correspondence: (P.G.); (G.D.); Tel.: +33-251125709 (P.G.); +33-240687880 (G.D.)
| | - Gaud Dervilly
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
- Correspondence: (P.G.); (G.D.); Tel.: +33-251125709 (P.G.); +33-240687880 (G.D.)
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18
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Pettini F, Visibelli A, Cicaloni V, Iovinelli D, Spiga O. Multi-Omics Model Applied to Cancer Genetics. Int J Mol Sci 2021; 22:ijms22115751. [PMID: 34072237 PMCID: PMC8199287 DOI: 10.3390/ijms22115751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Abstract
In this review, we focus on bioinformatic oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. Before providing a deeper insight into the bioinformatics approach and utilities involved in oncology, we must understand what is a system biology framework and the genetic connection, because of the high heterogenicity of the backgrounds of people approaching precision medicine. In fact, it is essential to providing general theoretical information on genomics, epigenomics, and transcriptomics to understand the phases of multi-omics approach. We consider how to create a multi-omics model. In the last section, we describe the new frontiers and future perspectives of this field.
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Affiliation(s)
- Francesco Pettini
- Department of Medical Biotechnology, University of Siena, Via M. Bracci 2, 53100 Siena, Italy
- Correspondence: ; Tel.: +39-3755461426
| | - Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (A.V.); (D.I.); (O.S.)
| | - Vittoria Cicaloni
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy;
| | - Daniele Iovinelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (A.V.); (D.I.); (O.S.)
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (A.V.); (D.I.); (O.S.)
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19
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Does the Phytochemical Diversity of Wild Plants Like the Erythrophleum genus Correlate with Geographical Origin? Molecules 2021; 26:molecules26061668. [PMID: 33802747 PMCID: PMC8002556 DOI: 10.3390/molecules26061668] [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: 02/23/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
Secondary metabolites are essential for plant survival and reproduction. Wild undomesticated and tropical plants are expected to harbor highly diverse metabolomes. We investigated the metabolomic diversity of two morphologically similar trees of tropical Africa, Erythrophleum suaveolens and E. ivorense, known for particular secondary metabolites named the cassaine-type diterpenoids. To assess how the metabolome varies between and within species, we sampled leaves from individuals of different geographic origins but grown from seeds in a common garden in Cameroon. Metabolites were analyzed using reversed phase LC-HRMS(/MS). Data were interpreted by untargeted metabolomics and molecular networks based on MS/MS data. Multivariate analyses enabled us to cluster samples based on species but also on geographic origins. We identified the structures of 28 cassaine-type diterpenoids among which 19 were new, 10 were largely specific to E. ivorense and five to E. suaveolens. Our results showed that the metabolome allows an unequivocal distinction of morphologically-close species, suggesting the potential of metabolite fingerprinting for these species. Plant geographic origin had a significant influence on relative concentrations of metabolites with variations up to eight (suaveolens) and 30 times (ivorense) between origins of the same species. This shows that the metabolome is strongly influenced by the geographical origin of plants (i.e., genetic factors).
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20
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Stodolna A, He M, Vasipalli M, Kingsbury Z, Becq J, Stockton JD, Dilworth MP, James J, Sillo T, Blakeway D, Ward ST, Ismail T, Ross MT, Beggs AD. Clinical-grade whole-genome sequencing and 3' transcriptome analysis of colorectal cancer patients. Genome Med 2021; 13:33. [PMID: 33632293 PMCID: PMC7908713 DOI: 10.1186/s13073-021-00852-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/11/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Colorectal cancer presents a difficult treatment paradigm, with over 40% of patients presenting at diagnosis with metastatic disease. We hypothesised that cWGS coupled with 3' transcriptome analysis would give new insights into colorectal cancer. METHODS Patients underwent PCR-free whole-genome sequencing and alignment and variant calling using a standardised pipeline to output SNVs, indels, SVs and CNAs. Additional insights into the mutational signatures and tumour biology were gained by the use of 3' RNA-seq. RESULTS Fifty-four patients were studied in total. Driver analysis identified the Wnt pathway gene APC as the only consistently mutated driver in colorectal cancer. Alterations in the PI3K/mTOR pathways were seen as previously observed in CRC. Multiple private CNAs, SVs and gene fusions were unique to individual tumours. Approximately 30% of patients had a tumour mutational burden of > 10 mutations/Mb of DNA, suggesting suitability for immunotherapy. CONCLUSIONS Clinical whole-genome sequencing offers a potential avenue for the identification of private genomic variation that may confer sensitivity to targeted agents and offer patients new options for targeted therapies.
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Affiliation(s)
- Agata Stodolna
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Miao He
- Illumina Cambridge, Granta Park, Cambridge, UK
| | | | | | | | - Joanne D Stockton
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Mark P Dilworth
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jonathan James
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Toju Sillo
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Daniel Blakeway
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Stephen T Ward
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Tariq Ismail
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Mark T Ross
- Illumina Cambridge, Granta Park, Cambridge, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, Vincent Drive, Birmingham, B15 2TT, UK.
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21
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Abstract
In recent years, mass spectrometry (MS)-based metabolomics has been extensively applied to characterize biochemical mechanisms, and study physiological processes and phenotypic changes associated with disease. Metabolomics has also been important for identifying biomarkers of interest suitable for clinical diagnosis. For the purpose of predictive modeling, in this chapter, we will review various supervised learning algorithms such as random forest (RF), support vector machine (SVM), and partial least squares-discriminant analysis (PLS-DA). In addition, we will also review feature selection methods for identifying the best combination of metabolites for an accurate predictive model. We conclude with best practices for reproducibility by including internal and external replication, reporting metrics to assess performance, and providing guidelines to avoid overfitting and to deal with imbalanced classes. An analysis of an example data will illustrate the use of different machine learning methods and performance metrics.
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Affiliation(s)
- Tusharkanti Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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22
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Hallam S, Stockton J, Bryer C, Whalley C, Pestinger V, Youssef H, Beggs AD. The transition from primary colorectal cancer to isolated peritoneal malignancy is associated with an increased tumour mutational burden. Sci Rep 2020; 10:18900. [PMID: 33144643 PMCID: PMC7641117 DOI: 10.1038/s41598-020-75844-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/13/2020] [Indexed: 12/31/2022] Open
Abstract
Colorectal Peritoneal metastases (CPM) develop in 15% of colorectal cancers. Cytoreductive surgery and heated intraperitoneal chemotherapy (CRS & HIPEC) is the current standard of care in selected patients with limited resectable CPM. Despite selection using known prognostic factors survival is varied and morbidity and mortality are relatively high. There is a need to improve patient selection and a paucity of research concerning the biology of isolated CPM. We aimed to determine the biology associated with transition from primary CRC to CPM and of patients with CPM not responding to treatment with CRS & HIPEC, to identify those suitable for treatment with CRS & HIPEC and to identify targets for existing repurposed or novel treatment strategies. A cohort of patients with CPM treated with CRS & HIPEC was recruited and divided according to prognosis. Molecular profiling of the transcriptome (n = 25), epigenome (n = 24) and genome (n = 21) of CPM and matched primary CRC was performed. CPM were characterised by frequent Wnt/ β catenin negative regulator mutations, TET2 mutations, mismatch repair mutations and high tumour mutational burden. Here we show the molecular features associated with CPM development and associated with not responding to CRS & HIPEC. Potential applications include improving patient selection for treatment with CRS & HIPEC and in future research into novel and personalised treatments targeting the molecular features identified here.
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Affiliation(s)
- Sally Hallam
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanne Stockton
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claire Bryer
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Celina Whalley
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Valerie Pestinger
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Haney Youssef
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Andrew D Beggs
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, B15 2TT, UK.
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23
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Liang D, Liu Q, Zhou K, Jia W, Xie G, Chen T. IP4M: an integrated platform for mass spectrometry-based metabolomics data mining. BMC Bioinformatics 2020; 21:444. [PMID: 33028191 PMCID: PMC7542974 DOI: 10.1186/s12859-020-03786-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background Metabolomics data analyses rely on the use of bioinformatics tools. Many integrated multi-functional tools have been developed for untargeted metabolomics data processing and have been widely used. More alternative platforms are expected for both basic and advanced users. Results Integrated mass spectrometry-based untargeted metabolomics data mining (IP4M) software was designed and developed. The IP4M, has 62 functions categorized into 8 modules, covering all the steps of metabolomics data mining, including raw data preprocessing (alignment, peak de-convolution, peak picking, and isotope filtering), peak annotation, peak table preprocessing, basic statistical description, classification and biomarker detection, correlation analysis, cluster and sub-cluster analysis, regression analysis, ROC analysis, pathway and enrichment analysis, and sample size and power analysis. Additionally, a KEGG-derived metabolic reaction database was embedded and a series of ratio variables (product/substrate) can be generated with enlarged information on enzyme activity. A new method, GRaMM, for correlation analysis between metabolome and microbiome data was also provided. IP4M provides both a number of parameters for customized and refined analysis (for expert users), as well as 4 simplified workflows with few key parameters (for beginners who are unfamiliar with computational metabolomics). The performance of IP4M was evaluated and compared with existing computational platforms using 2 data sets derived from standards mixture and 2 data sets derived from serum samples, from GC–MS and LC–MS respectively. Conclusion IP4M is powerful, modularized, customizable and easy-to-use. It is a good choice for metabolomics data processing and analysis. Free versions for Windows, MAC OS, and Linux systems are provided.
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Affiliation(s)
- Dandan Liang
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Quan Liu
- Human Metabolomics Institute, Inc., Shenzhen, 518109, Guangdong, China
| | - Kejun Zhou
- Human Metabolomics Institute, Inc., Shenzhen, 518109, Guangdong, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Guoxiang Xie
- Human Metabolomics Institute, Inc., Shenzhen, 518109, Guangdong, China.
| | - Tianlu Chen
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
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24
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Plyushchenko I, Shakhmatov D, Bolotnik T, Baygildiev T, Nesterenko PN, Rodin I. An approach for feature selection with data modelling in LC-MS metabolomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3582-3591. [PMID: 32701078 DOI: 10.1039/d0ay00204f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The data processing workflow for LC-MS based metabolomics study is suggested with signal drift correction, univariate analysis, supervised learning, feature selection and unsupervised modelling. The proposed approach requires only an annotation-free peak table and produces an extremely reduced set of the most relevant features together with validation via Receiver Operating Characteristic analysis for selected predictors, cross-validation and unsupervised projection. The presented study was initially optimised by its own experimental set and then was successfully tested by using 36 datasets from 21 publicly available metabolomics projects. The suggested workflow can be used for classification purposes in high dimensional metabolomics studies and as a first step in exploratory analysis, data projection, biomarker selection, data integration and fusion.
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Affiliation(s)
- Ivan Plyushchenko
- Lomonosov Moscow State University, Chemistry Department, 119992, GSP-2, Lenin Hills, 1b3, Moscow, Russia.
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25
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Benítez Del Castillo JM, Pinazo-Duran MD, Sanz-González SM, Muñoz-Hernández AM, Garcia-Medina JJ, Zanón-Moreno V. Tear 1H Nuclear Magnetic Resonance-Based Metabolomics Application to the Molecular Diagnosis of Aqueous Tear Deficiency and Meibomian Gland Dysfunction. Ophthalmic Res 2020; 64:297-309. [PMID: 32674101 DOI: 10.1159/000510211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/11/2020] [Indexed: 11/19/2022]
Abstract
PURPOSE Meibomian gland dysfunction (MGD) is a major cause of signs and symptoms related to dry eyes (DE) and eyelid inflammation. We investigated the composition of human tears by metabolomic approaches in patients with aqueous tear deficiency and MGD. METHODS Participants in this prospective, case-control pilot study were split into patients with aqueous tear deficiency and MGD (DE-MGD [n = 15]) and healthy controls (CG; n = 20). Personal interviews, ocular surface disease index (OSDI), and ophthalmic examinations were performed. Reflex tears collected by capillarity were processed to 1H nuclear magnetic resonance (NMR) spectroscopy and quantitative data analysis to identify molecules by spectra comparison to library entries of purified standards and/or unknown entities. Statistical analyses were made by the SPSS 22.0 program. RESULTS Chemometric analysis and 1H NMR spectra comparison revealed the presence of 60 metabolites in tears. Differentiating features were evident in the NMR spectra of the 2 clinical groups, characterized by significant upregulation of phenylalanine, glycerol, and isoleucine, and downregulation of glycoproteins, leucine, and -CH3 lipids, as compared to the CG. The 1H NMR metabolomic analyses of human tears confirmed the applicability of this platform with high predictive accuracy/reliability. CONCLUSIONS Our key distinctive findings support that DE-MGD induces tear metabolomics profile changes. Metabolites contributing to a higher separation from the CG can presumably be used, in the foreseeable future, as DE-MGD biomarkers for better managing the diagnosis and therapy of this disease.
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Affiliation(s)
- José Manuel Benítez Del Castillo
- Department of Ophthalmology, San Carlos Clinic Hospital, Madrid, Spain.,Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain
| | - Maria Dolores Pinazo-Duran
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain.,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain.,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
| | - Silvia M Sanz-González
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain.,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain.,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
| | - Ana M Muñoz-Hernández
- Department of Ophthalmology, San Carlos Clinic Hospital, Madrid, Spain.,Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain
| | - Jose J Garcia-Medina
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain.,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain.,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain.,Department of Ophthalmology, University Hospital Morales Meseguer, Murcia, Spain
| | - Vicente Zanón-Moreno
- Spanish Net of Ophthalmic Pathology (OFTARED) of the Institute of Health Carlos III, Madrid, Spain, .,Ophthalmic Research Unit "Santiago Grisolía"/FISABIO, Valencia, Spain, .,Cellular and Molecular Ophthalmo-Biology Group, Department of Surgery (Ophthalmology), Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain, .,International University of Valencia, Valencia, Spain,
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26
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Akter S, Xu D, Nagel SC, Bromfield JJ, Pelch KE, Wilshire GB, Joshi T. GenomeForest: An Ensemble Machine Learning Classifier for Endometriosis. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2020; 2020:33-42. [PMID: 32477621 PMCID: PMC7233069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Endometriosis is a complex and high impact disease affecting 176 million women worldwide with diagnostic latency between 4 to 11 years due to lack of a definitive clinical symptom or a minimally invasive diagnostic method. In this study, we developed a new ensemble machine learning classifier based on chromosomal partitioning, named GenomeForest and applied it in classifying the endometriosis vs. the control patients using 38 RNA-seq and 80 enrichment-based DNA-methylation (MBD-seq) datasets, and computed performance assessment with six different experiments. The ensemble machine learning models provided an avenue for identifying several candidate biomarker genes with a very high F1 score; a near perfect F1 score (0.968) for the transcriptomics dataset and a very high F1 score (0.918) for the methylomics dataset. We hope in the future a less invasive biopsy can be used to diagnose endometriosis using the findings from such ensemble machine learning classifiers, as demonstrated in this study.
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Affiliation(s)
| | - Dong Xu
- Informatics Institute
- Electrical Engineering and Computer Science
- Christopher S. Bond Life Sciences Center
| | - Susan C Nagel
- OB/GYN and Women's Health , University of Missouri, Columbia, MO
| | - John J Bromfield
- OB/GYN and Women's Health , University of Missouri, Columbia, MO
| | | | | | - Trupti Joshi
- Informatics Institute
- Christopher S. Bond Life Sciences Center
- Health Management and Informatics, University of Missouri, Columbia, MO
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27
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de Anda-Jáuregui G, Hernández-Lemus E. Computational Oncology in the Multi-Omics Era: State of the Art. Front Oncol 2020; 10:423. [PMID: 32318338 PMCID: PMC7154096 DOI: 10.3389/fonc.2020.00423] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/10/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is the quintessential complex disease. As technologies evolve faster each day, we are able to quantify the different layers of biological elements that contribute to the emergence and development of malignancies. In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological phenomena, and to move forward toward the precision medicine paradigm. In this review, we will focus on computational oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. We will discuss the current roles of computation in oncology in the context of multi-omic technologies, which include: data acquisition and processing; data management in the clinical and research settings; classification, diagnosis, and prognosis; and the development of models in the research setting, including their use for therapeutic target identification. We will discuss the machine learning and network approaches as two of the most promising emerging paradigms, in computational oncology. These approaches provide a foundation on how to integrate different layers of biological description into coherent frameworks that allow advances both in the basic and clinical settings.
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Affiliation(s)
- Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Cátedras Conacyt Para Jóvenes Investigadores, National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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A Data Mining Metabolomics Exploration of Glaucoma. Metabolites 2020; 10:metabo10020049. [PMID: 32012845 PMCID: PMC7074047 DOI: 10.3390/metabo10020049] [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: 12/02/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 01/08/2023] Open
Abstract
Glaucoma is an age related disease characterized by the progressive loss of retinal ganglion cells, which are the neurons that transduce the visual information from the retina to the brain. It is the leading cause of irreversible blindness worldwide. To gain further insights into primary open-angle glaucoma (POAG) pathophysiology, we performed a non-targeted metabolomics analysis on the plasma from POAG patients (n = 34) and age- and sex-matched controls (n = 30). We investigated the differential signature of POAG plasma compared to controls, using liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS). A data mining strategy, combining a filtering method with threshold criterion, a wrapper method with iterative selection, and an embedded method with penalization constraint, was used. These strategies are most often used separately in metabolomics studies, with each of them having their own limitations. We opted for a synergistic approach as a mean to unravel the most relevant metabolomics signature. We identified a set of nine metabolites, namely: nicotinamide, hypoxanthine, xanthine, and 1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline with decreased concentrations and N-acetyl-L-Leucine, arginine, RAC-glycerol 1-myristate, 1-oleoyl-RAC-glycerol, cystathionine with increased concentrations in POAG; the modification of nicotinamide, N-acetyl-L-Leucine, and arginine concentrations being the most discriminant. Our findings open up therapeutic perspectives for the diagnosis and treatment of POAG.
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Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites 2019; 9:E200. [PMID: 31548506 PMCID: PMC6835268 DOI: 10.3390/metabo9100200] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022] Open
Abstract
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.
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Affiliation(s)
- Jan Stanstrup
- Preventive and Clinical Nutrition, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark.
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany.
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
| | - Luca Nicolotti
- The Australian Wine Research Institute, Metabolomics Australia, PO Box 197, Adelaide SA 5064, Australia.
| | - Kristian Peters
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.
| | - Reza M Salek
- The International Agency for Research on Cancer, 150 cours Albert Thomas, CEDEX 08, 69372 Lyon, France.
| | - Tobias Schulze
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg.
| | - Michael A Stravs
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dubendorf, Switzerland.
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Sciences and Decision, MetaboHUB, Gif-Sur-Yvette F-91191, France.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Ralf J M Weber
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
- Chair of Analytical Food Chemistry, Technische Universität München, 85354 Weihenstephan, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig Deutscher, Platz 5e, 04103 Leipzig, Germany.
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Akter S, Xu D, Nagel SC, Bromfield JJ, Pelch K, Wilshire GB, Joshi T. Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data. Front Genet 2019; 10:766. [PMID: 31552087 PMCID: PMC6737999 DOI: 10.3389/fgene.2019.00766] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/19/2019] [Indexed: 12/29/2022] Open
Abstract
Endometriosis is a complex and common gynecological disorder yet a poorly understood disease affecting about 176 million women worldwide and causing significant impact on their quality of life and economic burden. Neither a definitive clinical symptom nor a minimally invasive diagnostic method is available, thus leading to an average of 4 to 11 years of diagnostic latency. Discovery of relevant biological patterns from microarray expression or next generation sequencing (NGS) data has been advanced over the last several decades by applying various machine learning tools. We performed machine learning analysis using 38 RNA-seq and 80 enrichment-based DNA methylation (MBD-seq) datasets. We experimented how well various supervised machine learning methods such as decision tree, partial least squares discriminant analysis (PLSDA), support vector machine, and random forest perform in classifying endometriosis from the control samples trained on both transcriptomics and methylomics data. The assessment was done from two different perspectives for improving classification performances: a) implication of three different normalization techniques and b) implication of differential analysis using the generalized linear model (GLM). Several candidate biomarker genes were identified by multiple machine learning experiments including NOTCH3, SNAPC2, B4GALNT1, SMAP2, DDB2, GTF3C5, and PTOV1 from the transcriptomics data analysis and TRPM6, RASSF2, TNIP2, RP3-522J7.6, FGD3, and MFSD14B from the methylomics data analysis. We concluded that an appropriate machine learning diagnostic pipeline for endometriosis should use TMM normalization for transcriptomics data, and quantile or voom normalization for methylomics data, GLM for feature space reduction and classification performance maximization.
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Affiliation(s)
- Sadia Akter
- Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Informatics Institute, University of Missouri, Columbia, MO, United States
- Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Susan C. Nagel
- OB/GYN and Women’s Health, University of Missouri School of Medicine, Columbia, MO, United States
| | - John J. Bromfield
- OB/GYN and Women’s Health, University of Missouri School of Medicine, Columbia, MO, United States
| | - Katherine Pelch
- OB/GYN and Women’s Health, University of Missouri School of Medicine, Columbia, MO, United States
| | | | - Trupti Joshi
- Informatics Institute, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Health Management and Informatics, University of Missouri, Columbia, MO, United States
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Van Loon E, Gazut S, Yazdani S, Lerut E, de Loor H, Coemans M, Noël LH, Thorrez L, Van Lommel L, Schuit F, Sprangers B, Kuypers D, Essig M, Gwinner W, Anglicheau D, Marquet P, Naesens M. Development and validation of a peripheral blood mRNA assay for the assessment of antibody-mediated kidney allograft rejection: A multicentre, prospective study. EBioMedicine 2019; 46:463-472. [PMID: 31378695 PMCID: PMC6710906 DOI: 10.1016/j.ebiom.2019.07.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Background Antibody-mediated rejection, a leading cause of renal allograft graft failure, is diagnosed by histological assessment of invasive allograft biopsies. Accurate non-invasive biomarkers are not available. Methods In the multicentre, prospective BIOMARGIN study, blood samples were prospectively collected at time of renal allograft biopsies between June 2011 and August 2016 and analyzed in three phases. The discovery and derivation phases of the study (N = 117 and N = 183 respectively) followed a case-control design and included whole genome transcriptomics and targeted mRNA expression analysis to construct and lock a multigene model. The primary end point was the diagnostic accuracy of the locked multigene assay for antibody-mediated rejection in a third validation cohort of serially collected blood samples (N = 387). This trial is registered with ClinicalTrials.gov, number NCT02832661. Findings We identified and locked an 8-gene assay (CXCL10, FCGR1A, FCGR1B, GBP1, GBP4, IL15, KLRC1, TIMP1) in blood samples from the discovery and derivation phases for discrimination between cases with (N = 49) and without (N = 134) antibody-mediated rejection. In the validation cohort, this 8-gene assay discriminated between cases with (N = 41) and without antibody-mediated rejection (N = 346) with good diagnostic accuracy (ROC AUC 79·9%; 95% CI 72·6 to 87·2, p < 0·0001). The diagnostic accuracy of the 8-gene assay was retained both at time of stable graft function and of graft dysfunction, within the first year and also later after transplantation. The 8-gene assay is correlated with microvascular inflammation and transplant glomerulopathy, but not with the histological lesions of T-cell mediated rejection. Interpretation We identified and validated a novel 8-gene expression assay that can be used for non-invasive diagnosis of antibody-mediated rejection. Funding The Seventh Framework Programme (FP7) of the European Commission.
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Affiliation(s)
- Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium
| | - Stéphane Gazut
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, Gif-sur-Yvette, France
| | - Saleh Yazdani
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Evelyne Lerut
- University Hospitals Leuven, Department of Morphology and Molecular Pathology, Leuven, Belgium
| | - Henriette de Loor
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Maarten Coemans
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Laure-Hélène Noël
- Necker-Enfants Malades Institute, French National Institute of Health and Medical Research U1151, France
| | - Lieven Thorrez
- KU Leuven Department of Development and Regeneration, campus KULAK, Kortrijk, Belgium
| | - Leentje Van Lommel
- KU Leuven Gene Expression Unit, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frans Schuit
- KU Leuven Gene Expression Unit, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium; KU Leuven Laboratory of Molecular Immunology, Rega Institute, Leuven, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium
| | - Marie Essig
- CHU Limoges, Department of Nephrology, Dialysis and Transplantation, Univ. Limoges, U850 INSERM, Limoges, France
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Dany Anglicheau
- Paris Descartes, Sorbonne Paris Cité University, INSERM U1151, Paris, France; Department of Nephrology and Kidney Transplantation, RTRS Centaure, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pierre Marquet
- CHU Limoges, Univ. Limoges, U850 INSERM, Limoges, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium.
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Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. PhenoMeNal: processing and analysis of metabolomics data in the cloud. Gigascience 2019; 8:giy149. [PMID: 30535405 PMCID: PMC6377398 DOI: 10.1093/gigascience/giy149] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/19/2018] [Accepted: 11/20/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. FINDINGS PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. CONCLUSIONS PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - James Bradbury
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marco Capuccini
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Timothy M D Ebbels
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Robert Glen
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, United Kingdom
| | - Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Ulrich L Günther
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Evangelos Handakas
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stephanie Herman
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | | | - Massimiliano Izzo
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Daniel Jacob
- INRA, University of Bordeaux, Plateforme Métabolome Bordeaux-MetaboHUB, 33140 Villenave d'Ornon, France
| | - David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
- Department of Informatics and Media, Uppsala University, Box 513, 751 20 Uppsala, Sweden
| | - Fabien Jourdan
- INRA - French National Institute for Agricultural Research, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ibrahim Karaman
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom
| | - Bita Khalili
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Payam Emami Khonsari
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | - Samuel Lampa
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Anders Larsson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Christian Ludwig
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jon Ander Novella
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jake T M Pearce
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Alina Peluso
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | | | | | - Michelle A C Reed
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence and CIRMMP, 50019 Sesto Fiorentino, Florence, Italy
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Noureddin Sadawi
- Department of Computer Science, College of Engineering, Design and Physical Sciences, Brunel University, London, UK
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Daniel Schober
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Mattia Tomasoni
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Merlijn van Rijswijk
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands
| | - Michael van Vliet
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | | | - Christoph Steinbeck
- Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
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Yazdani S, Callemeyn J, Gazut S, Lerut E, de Loor H, Wevers M, Heylen L, Saison C, Koenig A, Thaunat O, Thorrez L, Kuypers D, Sprangers B, Noël LH, Van Lommel L, Schuit F, Essig M, Gwinner W, Anglicheau D, Marquet P, Naesens M. Natural killer cell infiltration is discriminative for antibody-mediated rejection and predicts outcome after kidney transplantation. Kidney Int 2018; 95:188-198. [PMID: 30396694 DOI: 10.1016/j.kint.2018.08.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/26/2018] [Accepted: 08/16/2018] [Indexed: 12/14/2022]
Abstract
Despite partial elucidation of the pathophysiology of antibody-mediated rejection (ABMR) after kidney transplantation, it remains largely unclear which of the involved immune cell types determine disease activity and outcome. We used microarray transcriptomic data from a case-control study (n=95) to identify genes that are differentially expressed in ABMR. Given the co-occurrence of ABMR and T-cell-mediated rejection (TCMR), we built a bioinformatics pipeline to distinguish ABMR-specific mRNA markers. Differential expression of 503 unique genes was identified in ABMR, with significant enrichment of natural killer (NK) cell pathways. CIBERSORT (Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts) deconvolution analysis was performed to elucidate the corresponding cell subtypes and showed increased NK cell infiltration in ABMR in comparison to TCMR and normal biopsies. Other leukocyte types (including monocytes/macrophages, CD4 and CD8 T cells, and dendritic cells) were increased in rejection, but could not discriminate ABMR from TCMR. Deconvolution-based estimation of NK cell infiltration was validated using computerized morphometry, and specifically associated with glomerulitis and peritubular capillaritis. In an external data set of kidney transplant biopsies, activated NK cell infiltration best predicted graft failure amongst all immune cell subtypes and even outperformed a histologic diagnosis of acute rejection. These data suggest that NK cells play a central role in the pathophysiology of ABMR and graft failure after kidney transplantation.
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Affiliation(s)
- Saleh Yazdani
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Stéphane Gazut
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, Gif-sur-Yvette, France
| | - Evelyne Lerut
- Department of Morphology and Molecular Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Henriette de Loor
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Max Wevers
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Line Heylen
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Carole Saison
- U1111 INSERM, Lyon, France; Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot University Hospital, Lyon, France
| | - Alice Koenig
- U1111 INSERM, Lyon, France; Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot University Hospital, Lyon, France; Claude Bernard University (Lyon-1), Lyon, France
| | - Olivier Thaunat
- U1111 INSERM, Lyon, France; Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot University Hospital, Lyon, France; Claude Bernard University (Lyon-1), Lyon, France
| | - Lieven Thorrez
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Dirk Kuypers
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Ben Sprangers
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Laure-Hélène Noël
- Necker-Enfants Malades Institute, French National Institute of Health and Medical Research U1151, Paris, France
| | - Leentje Van Lommel
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frans Schuit
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Marie Essig
- CHU Limoges, Department of Nephrology, Dialysis and Transplantation, University of Limoges, Limoges, France
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Dany Anglicheau
- Necker-Enfants Malades Institute, French National Institute of Health and Medical Research U1151, Paris, France; Paris Descartes, Sorbonne Paris Cité University, Paris, France; Department of Nephrology and Kidney Transplantation, RTRS Centaure, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pierre Marquet
- U850 INSERM, University of Limoges, CHU Limoges, Limoges, France
| | - Maarten Naesens
- Laboratory of Nephrology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium.
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Blasco H, Patin F, Descat A, Garçon G, Corcia P, Gelé P, Lenglet T, Bede P, Meininger V, Devos D, Gossens JF, Pradat PF. A pharmaco-metabolomics approach in a clinical trial of ALS: Identification of predictive markers of progression. PLoS One 2018; 13:e0198116. [PMID: 29870556 PMCID: PMC5988280 DOI: 10.1371/journal.pone.0198116] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/14/2018] [Indexed: 12/17/2022] Open
Abstract
There is an urgent and unmet need for accurate biomarkers in Amyotrophic Lateral Sclerosis. A pharmaco-metabolomics study was conducted using plasma samples from the TRO19622 (olesoxime) trial to assess the link between early metabolomic profiles and clinical outcomes. Patients included in this trial were randomized into either Group O receiving olesoxime (n = 38) or Group P receiving placebo (n = 36). The metabolomic profile was assessed at time-point one (V1) and 12 months (V12) after the initiation of the treatment. High performance liquid chromatography coupled with tandem mass spectrometry was used to quantify 188 metabolites (Biocrates® commercial kit). Multivariate analysis based on machine learning approaches (i.e. Biosigner algorithm) was performed. Metabolomic profiles at V1 and V12 and changes in metabolomic profiles between V1 and V12 accurately discriminated between Groups O and P (p<5×10–6), and identified glycine, kynurenine and citrulline/arginine as the best predictors of group membership. Changes in metabolomic profiles were closely linked to clinical progression, and correlated with glutamine levels in Group P and amino acids, lipids and spermidine levels in Group O. Multivariate models accurately predicted disease progression and highlighted the discriminant role of sphingomyelins (SM C22:3, SM C24:1, SM OH C22:2, SM C16:1). To predict SVC from SM C24:1 in group O and SVC from SM OH C22:2 and SM C16:1 in group P+O, we noted a median sensitivity between 67% and 100%, a specificity between 66.7 and 71.4%, a positive predictive value between 66 and 75% and a negative predictive value between 70% and 100% in the test sets. This proof-of-concept study demonstrates that the metabolomics has a role in evaluating the biological effect of an investigational drug and may be a candidate biomarker as a secondary outcome measure in clinical trials.
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Affiliation(s)
- Hélène Blasco
- Université François-Rabelais, Inserm, Tours, France
- Laboratoire de Biochimie, CHRU de Tours, Tours, France
- * E-mail:
| | - Franck Patin
- Université François-Rabelais, Inserm, Tours, France
- Laboratoire de Biochimie, CHRU de Tours, Tours, France
| | - Amandine Descat
- Centre Universitaire de Mesures et d'Analyses (CUMA), EA, Université de Lille, Lille, France
| | - Guillaume Garçon
- Université de Lille, CHU Lille, Institut Pasteur de Lille, EA, IMPECS, Lille, France
| | - Philippe Corcia
- Université François-Rabelais, Inserm, Tours, France
- Centre SLA, Service de Neurologie, CHRU Bretonneau, Tours, France
| | - Patrick Gelé
- Centre d'Investigation Clinique, Université de Lille, Lille, France
| | - Timothée Lenglet
- Département des Maladies du Système Nerveux, Centre Référent Maladie Rare SLA, Hôpital de la Pitié-Salpétrière, Paris, France
| | - Peter Bede
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d’Imagerie Biomédicale,Paris, France
- Academic Unit of Neurology, Trinity College, Dublin, Ireland
| | | | - David Devos
- INSERM U1171, Pharmacologie Médicale & Neurologie, Université, Faculté de Médecine, CHU de Lille, Lille, France
| | - Jean François Gossens
- Centre Universitaire de Mesures et d'Analyses (CUMA), EA, Université de Lille, Lille, France
| | - Pierre-François Pradat
- Département des Maladies du Système Nerveux, Centre Référent Maladie Rare SLA, Hôpital de la Pitié-Salpétrière, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d’Imagerie Biomédicale,Paris, France
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute Ulster University, C-TRIC, Altnagelvin Hospital, Derry/Londonderry, United Kingdom
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35
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Metabolomics fingerprint of coffee species determined by untargeted-profiling study using LC-HRMS. Food Chem 2018; 245:603-612. [DOI: 10.1016/j.foodchem.2017.10.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/18/2017] [Accepted: 10/06/2017] [Indexed: 01/03/2023]
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Blasco H, Veyrat-Durebex C, Bocca C, Patin F, Vourc'h P, Kouassi Nzoughet J, Lenaers G, Andres CR, Simard G, Corcia P, Reynier P. Lipidomics Reveals Cerebrospinal-Fluid Signatures of ALS. Sci Rep 2017; 7:17652. [PMID: 29247199 PMCID: PMC5732162 DOI: 10.1038/s41598-017-17389-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/22/2017] [Indexed: 12/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS), the commonest adult-onset motor neuron disorder, is characterized by a survival span of only 2–5 years after onset. Relevant biomarkers or specific metabolic signatures would provide powerful tools for the management of ALS. The main objective of this study was to investigate the cerebrospinal fluid (CSF) lipidomic signature of ALS patients by mass spectrometry to evaluate the diagnostic and predictive values of the profile. We showed that ALS patients (n = 40) displayed a highly significant specific CSF lipidomic signature compared to controls (n = 45). Phosphatidylcholine PC(36:4), higher in ALS patients (p = 0.0003) was the most discriminant molecule, and ceramides and glucosylceramides were also highly relevant. Analysis of targeted lipids in the brain cortex of ALS model mice confirmed the role of some discriminant lipids such as PC. We also obtained good models for predicting the variation of the ALSFRS-r score from the lipidome baseline, with an accuracy of 71% in an independent set of patients. Significant predictions of clinical evolution were found to be correlated to sphingomyelins and triglycerides with long-chain fatty acids. Our study, which shows extensive lipid remodelling in the CSF of ALS patients, provides a new metabolic signature of the disease and its evolution with good predictive performance.
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Affiliation(s)
- H Blasco
- Université François-Rabelais, Inserm, U930, Tours, France. .,Laboratoire de Biochimie, CHRU de Tours, France. .,Institut MITOVASC, UMR CNRS6015-INSERM1083, Université d'Angers, Angers, France.
| | - C Veyrat-Durebex
- Institut MITOVASC, UMR CNRS6015-INSERM1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, France
| | - C Bocca
- Institut MITOVASC, UMR CNRS6015-INSERM1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, France
| | - F Patin
- Université François-Rabelais, Inserm, U930, Tours, France.,Laboratoire de Biochimie, CHRU de Tours, France
| | - P Vourc'h
- Université François-Rabelais, Inserm, U930, Tours, France.,Laboratoire de Biochimie, CHRU de Tours, France
| | | | - G Lenaers
- Département de Biochimie et Génétique, CHU d'Angers, France
| | - C R Andres
- Université François-Rabelais, Inserm, U930, Tours, France.,Laboratoire de Biochimie, CHRU de Tours, France
| | - G Simard
- Institut MITOVASC, UMR CNRS6015-INSERM1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, France
| | - P Corcia
- Université François-Rabelais, Inserm, U930, Tours, France.,Centre de Ressources et de Compétences SLA, Service de Neurologie, CHRU Bretonneau, Tours, France.,Fédération des CRCSLA Tours et Limoges, LITORALS, Limoges, France
| | - P Reynier
- Institut MITOVASC, UMR CNRS6015-INSERM1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, France
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Guitton Y, Tremblay-Franco M, Le Corguillé G, Martin JF, Pétéra M, Roger-Mele P, Delabrière A, Goulitquer S, Monsoor M, Duperier C, Canlet C, Servien R, Tardivel P, Caron C, Giacomoni F, Thévenot EA. Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics. Int J Biochem Cell Biol 2017; 93:89-101. [DOI: 10.1016/j.biocel.2017.07.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/14/2017] [Accepted: 07/10/2017] [Indexed: 12/11/2022]
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38
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Abstract
Data processing and analysis are major bottlenecks in high-throughput metabolomic experiments. Recent advancements in data acquisition platforms are driving trends toward increasing data size (e.g., petabyte scale) and complexity (multiple omic platforms). Improvements in data analysis software and in silico methods are similarly required to effectively utilize these advancements and link the acquired data with biological interpretations. Herein, we provide an overview of recently developed and freely available metabolomic tools, algorithms, databases, and data analysis frameworks. This overview of popular tools for MS and NMR-based metabolomics is organized into the following sections: data processing, annotation, analysis, and visualization. The following overview of newly developed tools helps to better inform researchers to support the emergence of metabolomics as an integral tool for the study of biochemistry, systems biology, environmental analysis, health, and personalized medicine.
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Affiliation(s)
- Biswapriya B Misra
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Johannes F Fahrmann
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, TX, USA
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