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Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:239. [PMID: 39169426 PMCID: PMC11337877 DOI: 10.1186/s13046-024-03141-5] [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: 05/20/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for around 90% of all oral cancers and is the eighth most common cancer worldwide. Despite progress in managing OSCC, the overall prognosis remains poor, with a survival rate of around 50-60%, largely due to tumor size and recurrence. The challenges of late-stage diagnosis and limitations in current methods emphasize the urgent need for less invasive techniques to enable early detection and treatment, crucial for improving outcomes in this aggressive form of oral cancer. Research is currently aimed at unraveling tumor-specific metabolite profiles to identify candidate biomarkers as well as discover underlying pathways involved in the onset and progression of cancer that could be used as new targets for diagnostic and therapeutic purposes. Metabolomics is an advanced technological approach to identify metabolites in different sample types (biological fluids and tissues). Since OSCC promotes metabolic reprogramming influenced by a combination of genetic predisposition and environmental factors, including tobacco and alcohol consumption, and viral infections, the identification of distinct metabolites through screening may aid in the diagnosis of this condition. Moreover, studies have shown the use of metabolites during the catalysis of epigenetic modification, indicating a link between epigenetics and metabolism. In this review, we will focus on the link between environmental, genetic, and epigenetic influences in metabolomic alterations in OSCC. In addition, we will discuss therapeutic targets of tumor metabolism, which may prevent oral tumor growth, metastasis, and drug resistance.
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Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Fariba Badrzadeh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Yuri Tsentalovich
- International tomography center CB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Institute for Genome Sciences, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
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2
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Lai H, Li G. Recent progress on media for biological sample preparation. J Chromatogr A 2024; 1734:465293. [PMID: 39181092 DOI: 10.1016/j.chroma.2024.465293] [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: 04/28/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
The analysis of biological samples is highly valuable for disease diagnosis and treatment, forensic examination, and public safety. However, the serious matrix interference effect generated by biological samples severely affects the analysis of trace analytes. Sample preparation methods are introduced to address the limitation by extracting, separating, enriching, purifying trace target analytes from biological samples. With the raising demand of biological sample analysis, a review focuses on media for biological sample preparation and analysis over the last 5 years is presented. High-performance media in biological sample preparation are first reviewed, including porous organic frameworks, imprinted polymers, hydrogels, ionic liquids, and bioactive media. Then, application of media for different biological sample preparation and analysis is briefly introduced, including liquid samples of body fluids, solid samples (hair, feces, and tissues), and gas samples of exhale breath gas. Finally, conclusions and outlooks on media promoting biological sample preparation are presented.
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Affiliation(s)
- Huasheng Lai
- Jiangxi Province Key Laboratory of Pharmacology of Traditional Chinese Medicine, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China; School of chemistry, Sun Yat-Sen University, Guangzhou, 510006, China.
| | - Gongke Li
- School of chemistry, Sun Yat-Sen University, Guangzhou, 510006, China.
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3
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Yazzie MT, Reitz ZL, Schmid R, Petras D, Aron AT. Native metabolomics for mass spectrometry-based siderophore discovery. Methods Enzymol 2024; 702:317-352. [PMID: 39155117 DOI: 10.1016/bs.mie.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Microorganisms, plants, and animals alike have specialized acquisition pathways for obtaining metals, with microorganisms and plants biosynthesizing and secreting small molecule natural products called siderophores and metallophores with high affinities and specificities for iron or other non-iron metals, respectively. This chapter details a novel approach to discovering metal-binding molecules, including siderophores and metallophores, from complex samples ranging from microbial supernatants to biological tissue to environmental samples. This approach, called Native Metabolomics, is a mass spectrometry method in which pH adjustment and metal infusion post-liquid chromatography are interfaced with ion identity molecular networking (IIMN). This rule-based data analysis workflow that enables the identification of metal-binding species based on defined mass (m/z) offsets with the same chromatographic profiles and retention times. Ion identity molecular networking connects compounds that are structurally similar by their fragmentation pattern and species that are ion adducts of the same compound by chromatographic shape correlations. This approach has previously revealed new insights into metal binding metabolites, including that yersiniabactin can act as a biological zincophore (in addition to its known role as a siderophore), that the recently elucidated lepotchelin natural products are cyanobacterial metallophores, and that antioxidants in traditional medicine bind iron. Native metabolomics can be conducted on any liquid chromatography-mass spectrometry system to explore the binding of any metal or multiple metals simultaneously, underscoring the potential for this method to become an essential strategy for elucidating biological metal-binding molecules.
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Affiliation(s)
- Marquis T Yazzie
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States
| | - Zachary L Reitz
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, United States
| | - Robin Schmid
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Daniel Petras
- Department of Biochemistry, University of California Riverside, Riverside, CA, United States; Interfaculty of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States.
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4
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Verdoodt F, Bhatti SFM, Kragic K, Van Ham L, Vanhaecke L, Hesta M, Hemeryck LY. Towards a better understanding of idiopathic epilepsy through metabolic fingerprinting of cerebrospinal fluid in dogs. Sci Rep 2024; 14:14750. [PMID: 38926488 PMCID: PMC11208596 DOI: 10.1038/s41598-024-64777-z] [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: 02/05/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Cerebrospinal fluid metabolomics is a promising research technology in the elucidation of nervous system disorders. Therefore, in this work, a cerebrospinal fluid (CSF) metabolomics method using liquid chromatography coupled to mass spectrometry was optimized and validated to cover a wide range of metabolites. An acceptable coefficient of variance regarding instrumental, within-lab and intra-assay precision was found for 95, 70 and 96 of 102 targeted metabolites, together with 1256, 676 and 976 untargeted compounds, respectively. Moreover, approximately 75% of targeted metabolites and 50% of untargeted compounds displayed good linearity across different dilution ranges. Consequently, metabolic alterations in CSF of dogs with idiopathic epilepsy (IE) were studied by comparing CSF of dogs diagnosed with IE (Tier II) to dogs with non-brain related disease. Targeted metabolome analysis revealed higher levels of cortisol, creatinine, glucose, hippuric acid, mannose, pantothenol, and 2-phenylethylamine (P values < 0.05) in CSF of dogs with IE, whereas CSF of dogs with IE showed lower levels of spermidine (P value = 0.02). Untargeted CSF metabolic fingerprints discriminated dogs with IE from dogs with non-brain related disease using Orthogonal Partial Least Squares Discriminant Analysis (R2(Y) = 0.997, Q2(Y) = 0.828), from which norepinephrine was putatively identified as an important discriminative metabolite.
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Affiliation(s)
- Fien Verdoodt
- Equine and Companion Animal Nutrition, Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Sofie F M Bhatti
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Karla Kragic
- Equine and Companion Animal Nutrition, Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Luc Van Ham
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Myriam Hesta
- Equine and Companion Animal Nutrition, Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Lieselot Y Hemeryck
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
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Hemmer S, Manier SK, Wagmann L, Meyer MR. Impact of four different extraction methods and three different reconstitution solvents on the untargeted metabolomics analysis of human and rat urine samples. J Chromatogr A 2024; 1725:464930. [PMID: 38696889 DOI: 10.1016/j.chroma.2024.464930] [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: 03/01/2024] [Revised: 04/08/2024] [Accepted: 04/21/2024] [Indexed: 05/04/2024]
Abstract
Unsuitable sample preparation may result in loss of important analytes and consequently affect the outcome of untargeted metabolomics. Due to species differences, different sample preparations may be required within the same biological matrix. The study aimed to compare the in-house sample preparation method for urine with methods from literature and to investigate the transferability of sample preparation from human urine to rat urine. A total of 12 different conditions for protein precipitation were tested, combining four different extraction solvents and three different reconstitution solvents using an untargeted liquid-chromatography high resolution mass spectrometry (LC-HRMS) metabolomics analysis. Evaluation was done based on the impact on feature count, their detectability, as well as the reproducibility of selected compounds. Results showed that a combination of methanol as extraction and acetonitrile/water (75/25) as reconstitution solvent provided improved results at least regarding the total feature count. Additionally, it was found that a higher amount of methanol was most suitable for extraction of rat urine among the tested conditions. In comparison, human urine requires significantly less volume of extraction solvent. Overall, it is recommended to systematically optimize both, the extraction method, and the reconstitution solvent for the used biofluid and the individual analytical settings.
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Affiliation(s)
- Selina Hemmer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Lea Wagmann
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany.
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Galineau L, Bourdin-Pintueles A, Bodard S, Busson J, Nadal-Desbarats L, Lefèvre A, Emond P, Mavel S. Temporal metabolomics state in pregnant rat: Analysis of amniotic fluid, placenta, and maternal plasma at embryonic and fetal time points. Placenta 2024; 150:22-30. [PMID: 38581971 DOI: 10.1016/j.placenta.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/08/2024]
Abstract
INTRODUCTION During pregnancy, the dynamic metabolic demands for fetal growth require a continuous supply of essential metabolites. Understanding maternal metabolome changes during gestation is crucial for predicting disease risks in neonates. METHODS The study aimed to characterize the placental and amniotic fluid (AF) metabolomes during gestation in rats at gestational days GD-13 and 19 reflecting the end of the embryonic and fetal periods, respectively, and the maternal plasma, using metabolomics (LC-MS) and chemometrics. The objective was to highlight, through univariate and multivariate analyses, the complementarity of the data obtained from these different biological matrices. RESULTS The biological matrix had more impact on the metabolome composition than the gestational stage. The placental and AF metabolomes showed specific metabolome evolving over the two gestational stages. Analyzing the three targeted metabolomes revealed evolving pathways in arginine and proline metabolism/glutathione metabolism and phenylalanine metabolism; purine metabolism; and carbohydrate metabolism. Significantly, lipid metabolism in the placenta exhibited substantial changes with higher levels of certain phosphatidylethanolamine and sphingomyelins at GD19 while some cholesteryl esters and some glycosphingolipids levels being in higher levels at GD13. DISCUSSION These data highlight the metabolic gradients (mainly in placenta, also in AF, but only a few in plasma) observed through embryonic patterning and organ development during mid-to late gestation.
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Affiliation(s)
- Laurent Galineau
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | | | - Sylvie Bodard
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | - Julie Busson
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | - Lydie Nadal-Desbarats
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France; PST-ASB, Université de Tours, France
| | - Antoine Lefèvre
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France; PST-ASB, Université de Tours, France
| | - Patrick Emond
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France; PST-ASB, Université de Tours, France; Service de Médecine Nucléaire In Vitro, CHRU Tours, Tours, France
| | - Sylvie Mavel
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France.
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Fang L, Zhai Q, Zhang H, Ji P, Chen C, Zhang H. Comparisons of different extraction methods and solvents for saliva samples. Metabolomics 2024; 20:38. [PMID: 38460055 DOI: 10.1007/s11306-024-02105-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 02/19/2024] [Indexed: 03/11/2024]
Abstract
INTRODUCTION Changes in the categories and concentrations of salivary metabolites may be closely related to oral, intestinal or systemic diseases. To study salivary metabolites, the first analytical step is to extract them from saliva samples as much as possible, while reducing interferences to a minimum. Frequently used extraction methods are protein precipitation (PPT), liquid-liquid extraction (LLE) and solid-phase extraction (SPE), with various organic solvents. The types and quantities of metabolites extracted with different methods may vary greatly, but few studies have systematically evaluated them. OBJECTIVES This study aimed to select the most suitable methods and solvents for the extraction of saliva according to different analytical targets. METHODS An untargeted metabolomics approach based on liquid chromatography-mass spectrometry was applied to obtain the raw data. The numbers of metabolites, repeatability of the data and intensities of mass spectrometry signals were used as evaluation criteria. RESULTS PPT resulted in the highest coverage. Among the PPT solvents, acetonitrile displayed the best repeatability and the highest coverage, while acetone resulted in the best signal intensities for the extracted compounds. LLE with the mixture of chloroform and methanol was the most suitable for the extraction of small hydrophobic compounds. CONCLUSION PPT with acetonitrile or acetone was recommended for untargeted analysis, while LLE with the mixture of chloroform and methanol was recommended for small hydrophobic compounds.
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Affiliation(s)
- Lingli Fang
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Qiming Zhai
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ping Ji
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Chang Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
| | - Hongmei Zhang
- Department of Pediatric Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China.
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de Souza HMR, Pereira TTP, de Sá HC, Alves MA, Garrett R, Canuto GAB. Critical Factors in Sample Collection and Preparation for Clinical Metabolomics of Underexplored Biological Specimens. Metabolites 2024; 14:36. [PMID: 38248839 PMCID: PMC10819689 DOI: 10.3390/metabo14010036] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
This review article compiles critical pre-analytical factors for sample collection and extraction of eight uncommon or underexplored biological specimens (human breast milk, ocular fluids, sebum, seminal plasma, sweat, hair, saliva, and cerebrospinal fluid) under the perspective of clinical metabolomics. These samples are interesting for metabolomics studies as they reflect the status of living organisms and can be applied for diagnostic purposes and biomarker discovery. Pre-collection and collection procedures are critical, requiring protocols to be standardized to avoid contamination and bias. Such procedures must consider cleaning the collection area, sample stimulation, diet, and food and drug intake, among other factors that impact the lack of homogeneity of the sample group. Precipitation of proteins and removal of salts and cell debris are the most used sample preparation procedures. This review intends to provide a global view of the practical aspects that most impact results, serving as a starting point for the designing of metabolomic experiments.
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Affiliation(s)
- Hygor M. R. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
| | - Tássia T. P. Pereira
- Departamento de Genética, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Hanna C. de Sá
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
| | - Marina A. Alves
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil;
| | - Rafael Garrett
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
- Department of Laboratory Medicine, Boston Children’s Hospital—Harvard Medical School, Boston, MA 02115, USA
| | - Gisele A. B. Canuto
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
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Lee BL, Rout M, Mandal R, Wishart DS. Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:705-717. [PMID: 37265043 DOI: 10.1002/mrc.5372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023]
Abstract
We report the development of a software program, called MagMet-F, that automates the processing and quantification of 1D 1 H NMR of human fecal extracts. To optimize the program, we identified 82 potential fecal metabolites using 1D 1 H NMR of six human fecal extracts using manual profiling and a literature review of known fecal metabolites. We acquired pure versions of those metabolites and then acquired their 1D 1 H NMR spectra at 700 MHz to generate a fecal metabolite spectral library for MagMet-F. The fitting of these metabolites by MagMet-F was iteratively optimized to replicate manual profiling. We validated MagMet-F's automated profiling using a test set of six fecal extracts. It correctly identified 80% of the compounds and quantified those within <20% of the values determined by manual profiling using Chenomx. We also compared MagMet-F's profiling performance to two other open-access NMR profiling tools, Bayesil and Batman. MagMet-F outperformed both. Bayesil repeatedly overestimated metabolite concentrations by 10% to 40% while Batman was unable to properly quantify any compounds and took 10-20× longer. We have implemented MagMet-F as a freely accessible web server to enable automated, fast and convenient 1D 1 H NMR spectral profiling of fecal samples. MagMet-F is available at https://www.magmet.ca.
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Affiliation(s)
- Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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San Nicolas M, Villate A, Olivares M, Etxebarria N, Zuloaga O, Aizpurua-Olaizola O, Usobiaga A. Exploratory optimisation of a LC-HRMS based analytical method for untargeted metabolomic screening of Cannabis Sativa L. through Data Mining. Anal Chim Acta 2023; 1279:341848. [PMID: 37827627 DOI: 10.1016/j.aca.2023.341848] [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: 06/27/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Recent increase in public acceptance of cannabis as a natural medical alternative for certain neurological pathologies has led to its approval in different regions of the world. However, due to its previous illegal background, little research has been conducted around its biochemical insights. Therefore, in the current framework, metabolomics may be a suitable approach for deepening the knowledge around this plant species. Nevertheless, experimental methods in metabolomics must be carefully handled, as slight modifications can lead to metabolomic coverage loss. Hence, the main objective of this work was to optimise an analytical method for appropriate untargeted metabolomic screening of cannabis. RESULTS We present an empirically optimised experimental procedure through which the broadest metabolomic coverage was obtained, in which extraction solvents for metabolite isolation, chromatographic columns for LC-qOrbitrap analysis and plant-representative biological tissues were compared. By exploratory means, it was determined that the solvent combination composed of CHCl3:H2O:CH3OH (2:1:1, v/v) provided the highest number of features from diverse chemical classes, as it was a two-phase extractant. In addition, a reverse phase 2.6 μm C18 100 Å (150 × 3 mm) chromatographic column was determined as the appropriate choice for adequate separation and further detection of the diverse metabolite classes. Apart from that, overall chromatographic peak quality provided by each column was observed and the need for batch correction methods through quality control (QC) samples was confirmed. At last, leaf and flower tissues resulted to provide complementary metabolic information of the plant, to the detriment of stem tissue, which resulted to be negligible. SIGNIFICANCE It was concluded that the optimised experimental procedure could significantly ease the path for future research works related to cannabis metabolomics by LC-HRMS means, as the work was based on previous plant metabolomics literature. Furthermore, it is crucial to highlight that an optimal analytical method can vary depending on the main objective of the research, as changes in the experimental factors can lead to different outcomes, regardless of whether the results are better or worse.
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Affiliation(s)
- M San Nicolas
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain.
| | - A Villate
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain
| | - M Olivares
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain
| | - N Etxebarria
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain
| | - O Zuloaga
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain
| | | | - A Usobiaga
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain
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Martín-Masot R, Jiménez-Muñoz M, Herrador-López M, Navas-López VM, Obis E, Jové M, Pamplona R, Nestares T. Metabolomic Profiling in Children with Celiac Disease: Beyond the Gluten-Free Diet. Nutrients 2023; 15:2871. [PMID: 37447198 DOI: 10.3390/nu15132871] [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: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Celiac disease (CD) is included in the group of complex or multifactorial diseases, i.e., those caused by the interaction of genetic and environmental factors. Despite a growing understanding of the pathophysiological mechanisms of the disease, diagnosis is still often delayed and there are no effective biomarkers for early diagnosis. The only current treatment, a gluten-free diet (GFD), can alleviate symptoms and restore intestinal villi, but its cellular effects remain poorly understood. To gain a comprehensive understanding of CD's progression, it is crucial to advance knowledge across various scientific disciplines and explore what transpires after disease onset. Metabolomics studies hold particular significance in unravelling the complexities of multifactorial and multisystemic disorders, where environmental factors play a significant role in disease manifestation and progression. By analyzing metabolites, we can gain insights into the reasons behind CD's occurrence, as well as better comprehend the impact of treatment initiation on patients. In this review, we present a collection of articles that showcase the latest breakthroughs in the field of metabolomics in pediatric CD, with the aim of trying to identify CD biomarkers for both early diagnosis and treatment monitoring. These advancements shed light on the potential of metabolomic analysis in enhancing our understanding of the disease and improving diagnostic and therapeutic strategies. More studies need to be designed to cover metabolic profiles in subjects at risk of developing the disease, as well as those analyzing biomarkers for follow-up treatment with a GFD.
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Affiliation(s)
- Rafael Martín-Masot
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
- Institute of Nutrition and Food Technology "José MataixVerdú" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18071 Granada, Spain
| | - María Jiménez-Muñoz
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
| | - Marta Herrador-López
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
| | - Víctor Manuel Navas-López
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
| | - Elia Obis
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), 25198 Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), 25198 Lleida, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), 25198 Lleida, Spain
| | - Teresa Nestares
- Institute of Nutrition and Food Technology "José MataixVerdú" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18071 Granada, Spain
- Department of Physiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
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12
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Fonseca TH, Von Rekowski CP, Araújo R, Oliveira MC, Justino G, Bento L, Calado CRC. The Impact of the Serum Extraction Protocol on Metabolomic Profiling Using UPLC-MS/MS and FTIR Spectroscopy. ACS OMEGA 2023; 8:20755-20766. [PMID: 37323376 PMCID: PMC10237515 DOI: 10.1021/acsomega.3c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Biofluid metabolomics is a very appealing tool to increase the knowledge associated with pathophysiological mechanisms leading to better and new therapies and biomarkers for disease diagnosis and prognosis. However, due to the complex process of metabolome analysis, including the metabolome isolation method and the platform used to analyze it, there are diverse factors that affect metabolomics output. In the present work, the impact of two protocols to extract the serum metabolome, one using methanol and another using a mixture of methanol, acetonitrile, and water, was evaluated. The metabolome was analyzed by ultraperformance liquid chromatography associated with tandem mass spectrometry (UPLC-MS/MS), based on reverse-phase and hydrophobic chromatographic separations, and Fourier transform infrared (FTIR) spectroscopy. The two extraction protocols of the metabolome were compared over the analytical platforms (UPLC-MS/MS and FTIR spectroscopy) concerning the number of features, the type of features, common features, and the reproducibility of extraction replicas and analytical replicas. The ability of the extraction protocols to predict the survivability of critically ill patients hospitalized at an intensive care unit was also evaluated. The FTIR spectroscopy platform was compared to the UPLC-MS/MS platform and, despite not identifying metabolites and consequently not contributing as much as UPLC-MS/MS in terms of information concerning metabolic information, it enabled the comparison of the two extraction protocols as well as the development of very good predictive models of patient's survivability, such as the UPLC-MS/MS platform. Furthermore, FTIR spectroscopy is based on much simpler procedures and is rapid, economic, and applicable in the high-throughput mode, i.e., enabling the simultaneous analysis of hundreds of samples in the microliter range in a couple of hours. Therefore, FTIR spectroscopy represents a very interesting complementary technique not only to optimize processes as the metabolome isolation but also for obtaining biomarkers such as those for disease prognosis.
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Affiliation(s)
- Tiago
A. H. Fonseca
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Cristiana P. Von Rekowski
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Rúben Araújo
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - M. Conceição Oliveira
- Centro
de Química Estrutural, Institute of Molecular Sciences, Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal
| | - Gonçalo
C. Justino
- Centro
de Química Estrutural, Institute of Molecular Sciences, Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal
| | - Luís Bento
- Intensive
Care Department, Centro Hospitalar Universitário
de Lisboa Central (CHULC), Rua José António Serrano, 1150-199 Lisboa, Portugal
- Integrated
Pathophysiological Mechanisms, CHRC, NOVA Medical School, Faculdade
de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Cecília R. C. Calado
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
- Centro
de Investigação em Modelação e Optimização
de Sistemas Multifuncionais (CIMOSM), Instituto Superior de Engenharia
de Lisboa (ISEL), Instituto Politécnico
de Lisboa, Rua Conselheiro
Emídio Navarro 1, 1959-007 Lisboa, Portugal
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13
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Brito de Oliveira Moreira O, Queiroz de Souza JC, Beraldo Candido JM, Patrícia do Nascimento M, Chellini PR, Marco de Lemos L, Leal de Oliveira MA. Factorial design applied to LC-ESI-QTOF mass spectrometer parameters for untargeted metabolomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2512-2521. [PMID: 37184618 DOI: 10.1039/d3ay00094j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Investigations of untargeted metabolomics are based on high-quality data acquisition usually from multiplatform systems that include high-resolution mass spectrometry equipment. The comprehensive set of results is used as data entry for bioinformatics and machine learning sciences to access reliable metabolic and biochemical information for clinical, forensic, environmental, and endless applications. In this context, design of experiments is a powerful tool for optimizing data acquisition procedures, using a multivariate approach, which enables the maximization of a high-quality amount of information with reduced number of tests. In this study, we applied a 33 Box-Behnken factorial design with central point triplicate for optimizing the ionization of an HPLC-ESI-QTOF method used for screening urine samples. Nozzle voltage (V), fragmentor voltage (V) and nebulizer pressure (psig) were the factors selected for variation. The response surface methodology was applied in the molecular features extracted at each level, resulting in a statistical model that helps evaluating the synergic interaction between these factors. Together with the qualitative analysis of the resulting total ion chromatograms, we came across a reproducible (6.14% RSD) and highly efficient method for untargeted metabolomics of human urine samples. The proposed method can be useful for applications in several urine-based metabolomics-driven studies, as the factorial design can be applied in the development of any analytical protocol considering different LC-MS setups.
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Affiliation(s)
- Olívia Brito de Oliveira Moreira
- Grupo de Química Analítica e Quimiometria - GQAQ, Chemistry Department, Institute of Exact Sciences, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil.
| | - Jéssica Cordeiro Queiroz de Souza
- Grupo de Química Analítica e Quimiometria - GQAQ, Chemistry Department, Institute of Exact Sciences, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil.
| | - João Marcos Beraldo Candido
- Grupo de Química Analítica e Quimiometria - GQAQ, Chemistry Department, Institute of Exact Sciences, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil.
| | - Maria Patrícia do Nascimento
- Grupo de Química Analítica e Quimiometria - GQAQ, Chemistry Department, Institute of Exact Sciences, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil.
| | - Paula Rocha Chellini
- Grupo de Química Analítica e Quimiometria - GQAQ, Chemistry Department, Institute of Exact Sciences, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil.
- Faculdade de Farmácia, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil
| | | | - Marcone Augusto Leal de Oliveira
- Grupo de Química Analítica e Quimiometria - GQAQ, Chemistry Department, Institute of Exact Sciences, Federal University of Juiz de Fora (UFJF), 36026-900, Juiz de Fora, MG, Brazil.
- National Institute of Science and Technology for Bioanalytics - INCTBio, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Campinas, SP, Brazil
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Ribay V, Praud C, Letertre MPM, Dumez JN, Giraudeau P. Hyperpolarized NMR metabolomics. Curr Opin Chem Biol 2023; 74:102307. [PMID: 37094508 DOI: 10.1016/j.cbpa.2023.102307] [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: 12/07/2022] [Revised: 02/20/2023] [Accepted: 03/21/2023] [Indexed: 04/26/2023]
Abstract
Hyperpolarized NMR is a promising approach to address the sensitivity limits of conventional NMR metabolomics approaches, which currently fails to detect minute metabolite concentrations in biological samples. This review describes how tremendous signal enhancement offered by dissolution-dynamic nuclear polarization and parahydrogen-based techniques can be fully exploited for molecular omics sciences. Recent developments, including the combination of hyperpolarization techniques with fast multi-dimensional NMR implementation and quantitative workflows are described, and a comprehensive comparison of existing hyperpolarization techniques is proposed. High-throughput, sensitivity, resolution and other relevant challenges that should be tackled for a general application of hyperpolarized NMR in metabolomics are discussed.
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Affiliation(s)
- Victor Ribay
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Clément Praud
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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15
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Saliva Metabolomic Profile in Dental Medicine Research: A Narrative Review. Metabolites 2023; 13:metabo13030379. [PMID: 36984819 PMCID: PMC10052075 DOI: 10.3390/metabo13030379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Metabolomic research tends to increase in popularity over the years, leading to the identification of new biomarkers related to specific health disorders. Saliva is one of the most newly introduced and systematically developed biofluids in the human body that can serve as an informative substance in the metabolomic profiling armamentarium. This review aims to analyze the current knowledge regarding the human salivary metabolome, its alterations due to physiological, environmental and external factors, as well as the limitations and drawbacks presented in the most recent research conducted, focusing on pre—analytical and analytical workflows. Furthermore, the use of the saliva metabolomic profile as a promising biomarker for several oral pathologies, such as oral cancer and periodontitis will be investigated.
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16
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Moreau C, El Habnouni C, Lecron JC, Morel F, Delwail A, Le Gall-Ianotto C, Le Garrec R, Misery L, Piver E, Vaillant L, Lefevre A, Emond P, Blasco H, Samimi M. Salivary metabolome indicates a shift in tyrosine metabolism in patients with burning mouth syndrome: a prospective case-control study. Pain 2023; 164:e144-e156. [PMID: 35916738 DOI: 10.1097/j.pain.0000000000002733] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022]
Abstract
ABSTRACT The pathophysiology of primary burning mouth syndrome (BMS) remains controversial. Targeted analyses or "omics" approach of saliva provide diagnostic or pathophysiological biomarkers. This pilot study's primary objective was to explore the pathophysiology of BMS through a comparative analysis of the salivary metabolome among 26 BMS female cases and 25 age- and sex-matched control subjects. Secondary objectives included comparative analyses of inflammatory cytokines, neuroinflammatory markers, and steroid hormones among cases and control subjects, and among BMS patients according to their clinical characteristics. Salivary metabolome, neuroinflammatory markers, cytokines, and steroids were, respectively, analysed by liquid chromatography coupled with mass spectrometry, ELISA and protease activity assay, and multiparametric Luminex method. Among the 166 detected metabolites, univariate analysis did not find any discriminant metabolite between groups. Supervised multivariate analysis divided patients into 2 groups with an accuracy of 60% but did not allow significant discrimination (permutation test, P = 0.35). Among the metabolites contributing to the model, 3 belonging to the tyrosine pathway ( l -dopa, l -tyrosine, and tyramine) were involved in the discrimination between cases and control subjects, and among BMS patients according to their levels of pain. Among the detectable molecules, levels of cytokines, steroid hormones, and neuroinflammatory markers did not differ between cases and control subjects and were not associated with characteristics of BMS patients. These results do not support the involvement of steroid hormones, inflammatory cytokines, or inflammatory neurogenic mediators in the pathophysiology of pain in BMS, whereas the observed shift in tyrosine metabolism may indicate an adaptative response to chronic pain or an impaired dopaminergic transmission.
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Affiliation(s)
- Charlotte Moreau
- University François Rabelais, Tours, France
- Department of Dermatology, University Hospital of Tours, Tours Cedex, France
| | - Chakib El Habnouni
- University François Rabelais, Tours, France
- Department of Dermatology, University Hospital of Tours, Tours Cedex, France
| | - Jean-Claude Lecron
- Laboratory Inflammation, Tissus Epithéliaux et Cytokines, Poitiers University and Immunology/inflammation Laboratory, Poitiers University Hospital, Poitiers, France
| | - Franck Morel
- Laboratory Inflammation, Tissus Epithéliaux et Cytokines, Poitiers University and Immunology/inflammation Laboratory, Poitiers University Hospital, Poitiers, France
| | - Adriana Delwail
- ImageUP, Plate-forme d'Imagerie and Laboratoire Signalisation et Transport Ioniques Membranaires ERL CNRS 7003/EA 7349, Poitiers University, Poitiers, France
| | | | - Raphaele Le Garrec
- Univ Brest, LIEN (Laboratoire Interactions Epithelium Neurones), Brest, France
| | - Laurent Misery
- Univ Brest, LIEN (Laboratoire Interactions Epithelium Neurones), Brest, France
| | - Eric Piver
- Department of Biochemistry and Molecular Biology, University Hospital of Tours, Tours Cedex, France
- Inserm UMR 1259-Morphogenèse et antigénicité du VIH et des virus des hépatites (MAVIVH)
| | - Loïc Vaillant
- University François Rabelais, Tours, France
- Department of Dermatology, University Hospital of Tours, Tours Cedex, France
| | | | - Patrick Emond
- UMR 1253 iBrain, Université de Tours, Inserm, Tours, France
- Department of In Vitro Nuclear Medicine, University Hospital of Tours, Tours Cedex, France
| | - Hélène Blasco
- Department of Biochemistry and Molecular Biology, University Hospital of Tours, Tours Cedex, France
- UMR 1253 iBrain, Université de Tours, Inserm, Tours, France
| | - Mahtab Samimi
- University François Rabelais, Tours, France
- Department of Dermatology, University Hospital of Tours, Tours Cedex, France
- BIP, 1282 INRA University of Tours, Tours, France
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17
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Krishnan S, Kanthaje S, Punchappady DR, Mujeeburahiman M, Ratnacaram CK. Circulating metabolite biomarkers: a game changer in the human prostate cancer diagnosis. J Cancer Res Clin Oncol 2023; 149:951-967. [PMID: 35764700 DOI: 10.1007/s00432-022-04113-y] [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: 04/20/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Prostate cancer (PCa) is the second most commonly diagnosed cancer in men in Western and Asian countries. Serum prostate-specific antigen (PSA) test has been the routine diagnostic method despite the tremendous research in diagnostic markers for early detection of PCa. A shift towards a promising and potential biomarker for PCa detection is through metabolomic profiling of biofluids, particularly the blood and urine samples. Finding reliable, routinely usable circulating metabolite biomarkers may not be a distant reality. METHODS We performed a PubMed-based literature search of metabolite biomarkers in blood and urine for the early detection of prostate cancer. The timeline of these searches was limited between 2007 and 2022 and the following keywords were used: 'metabolomics', 'liquid biopsy', 'circulating metabolites', 'serum metabolite', 'plasma metabolite', and 'urine metabolite' with respect to 'prostate cancer'. We focussed only on diagnosis-based studies with only the subject-relevant articles published in the English language and excluded all of the other irrelevant publications that included prostate tissue biomarkers and cell line biomarkers. RESULTS We have consolidated all the blood and urine-based potential metabolite candidates in individual as well as panels, including lipid classes, fatty acids, amino acids, and volatile organic compounds which may become useful for PCa diagnosis. CONCLUSION All these metabolome findings unveil the impact of different dimensions of PCa development, giving a promising strategy to diagnose the disease since suspected individuals can be subjected to repeated and largescale blood and urine testing.
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Affiliation(s)
- Sabareeswaran Krishnan
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India
- Department of Urology, Yenepoya Medical College Hospital, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Shruthi Kanthaje
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Devasya Rekha Punchappady
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - M Mujeeburahiman
- Department of Urology, Yenepoya Medical College Hospital, Deralakatte, Mangaluru, 575018, Karnataka, India.
| | - Chandrahas Koumar Ratnacaram
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India.
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18
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Tran C, Horyanto D, Stanley D, Cock IE, Chen X, Feng Y. Antimicrobial Properties of Bacillus Probiotics as Animal Growth Promoters. Antibiotics (Basel) 2023; 12:407. [PMID: 36830317 PMCID: PMC9952206 DOI: 10.3390/antibiotics12020407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Antibiotic growth promoters (AGPs) suppress the growth of infectious pathogens. These pathogens negatively impact agricultural production worldwide and often cause health problems if left untreated. Here, we evaluate six Bacillus strains (BPR-11, BPR-12, BPR-13, BPR-14, BPR-16 and BPR-17), which are known for their ability to survive harsh environmental conditions, as AGP replacements in animal feed. Four of these Bacillus strains (BPR-11, BPR-14, BPR-16 and BPR-17) showed antimicrobial activity against the pathogenic strains Clostridium perfringens, Escherichia coli and Staphylococcus aureus at 25 μg/mL, with BPR-16 and BPR-17 also able to inhibit Pseudomonas aeruginosa and Salmonella enterica at 100 μg/mL. Further chemical investigation of BPR-17 led to the identification of eight metabolites, namely C16, C15, C14 and C13 surfactin C (1-4), maculosin (5), maculosine 2 (6), genistein (7) and daidzein (8). Purified compounds (1-4) were able to inhibit all the tested pathogens with MIC values ranging from 6.25 to 50 μg/mL. Maculosin (5) and maculosine 2 (6) inhibited C. perfringens, E. coli and S. aureus with an MIC of 25 μg/mL while genistein (7) and daidzein (8) showed no activity. An animal trial involving feeding BPR-11, BPR-16 and BPR-17 to a laboratory poultry model led to an increase in animal growth, and a decrease in feed conversion ratio and mortality. The presence of surfactin C analogues (3-4) in the gut following feeding with probiotics was confirmed using an LC-MS analysis. The investigation of these Bacillus probiotics, their metabolites, their impacts on animal performance indicators and their presence in the gastrointestinal system illustrates that these probiotics are effective alternatives to AGPs.
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Affiliation(s)
- Charlie Tran
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, QLD 4111, Australia;
| | - Darwin Horyanto
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD 4702, Australia; (D.H.); (D.S.)
- Bioproton Pty Ltd., Brisbane, QLD 4110, Australia;
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD 4702, Australia; (D.H.); (D.S.)
| | - Ian E. Cock
- School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia;
| | | | - Yunjiang Feng
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, QLD 4111, Australia;
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Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24021354. [PMID: 36674867 PMCID: PMC9865896 DOI: 10.3390/ijms24021354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/13/2023] Open
Abstract
Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis, and for developing a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently-used solvent systems: chloroform/methanol and methanol-only. Whole blood samples were collected from participants (n = 6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods: (i) methanol precipitation and (ii) 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.
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20
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Wu X, Wang Z, Luo L, Shu D, Wang K. Metabolomics in hepatocellular carcinoma: From biomarker discovery to precision medicine. FRONTIERS IN MEDICAL TECHNOLOGY 2023; 4:1065506. [PMID: 36688143 PMCID: PMC9845953 DOI: 10.3389/fmedt.2022.1065506] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains a global health burden, and is mostly diagnosed at late and advanced stages. Currently, limited and insensitive diagnostic modalities continue to be the bottleneck of effective and tailored therapy for HCC patients. Moreover, the complex reprogramming of metabolic patterns during HCC initiation and progression has been obstructing the precision medicine in clinical practice. As a noninvasive and global screening approach, metabolomics serves as a powerful tool to dynamically monitor metabolic patterns and identify promising metabolite biomarkers, therefore holds a great potential for the development of tailored therapy for HCC patients. In this review, we summarize the recent advances in HCC metabolomics studies, including metabolic alterations associated with HCC progression, as well as novel metabolite biomarkers for HCC diagnosis, monitor, and prognostic evaluation. Moreover, we highlight the application of multi-omics strategies containing metabolomics in biomarker discovery for HCC. Notably, we also discuss the opportunities and challenges of metabolomics in nowadays HCC precision medicine. As technologies improving and metabolite biomarkers discovering, metabolomics has made a major step toward more timely and effective precision medicine for HCC patients.
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Affiliation(s)
- Xingyun Wu
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zihao Wang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Li Luo
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Dan Shu
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China,Correspondence: Kui Wang Dan Shu
| | - Kui Wang
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, China,Correspondence: Kui Wang Dan Shu
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21
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Grootveld M, Page G, Bhogadia M, Hunwin K, Edgar M. Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part III: Implementations for the Diagnosis of Non-Cancerous Disorders, Both Oral and Systemic. Metabolites 2023; 13:metabo13010066. [PMID: 36676991 PMCID: PMC9864626 DOI: 10.3390/metabo13010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
This communication represents Part III of our series of reports based on the applications of human saliva as a useful and conveniently collectable medium for the discovery, identification and monitoring of biomarkers, which are of some merit for the diagnosis of human diseases. Such biomarkers, or others reflecting the dysfunction of specific disease-associated metabolic pathways, may also be employed for the prognostic pathological tracking of these diseases. Part I of this series set the experimental and logistical groundwork for this report, and the preceding paper, Part II, featured the applications of newly developed metabolomics technologies to the diagnosis and severity grading of human cancer conditions, both oral and systemic. Clearly, there are many benefits, both scientific and economic, associated with the donation of human saliva samples (usually as whole mouth saliva) from humans consenting to and participating in investigations focused on the discovery of biomolecular markers of diseases. These include usually non-invasive collection protocols, relatively low cost when compared against blood sample collection, and no requirement for clinical supervision during collection episodes. This paper is centred on the employment and value of 'state-of-the-art' metabolomics technologies to the diagnosis and prognosis of a wide range of non-cancerous human diseases. Firstly, these include common oral diseases such as periodontal diseases (from type 1 (gingivitis) to type 4 (advanced periodontitis)), and dental caries. Secondly, a wide range of extra-oral (systemic) conditions are covered, most notably diabetes types 1 and 2, cardiovascular and neurological diseases, and Sjögren's syndrome, along with a series of viral infections, e.g., pharyngitis, influenza, HIV and COVID-19. Since the authors' major research interests lie in the area of the principles and applications of NMR-linked metabolomics techniques, many, but not all, of the studies reviewed were conducted using these technologies, with special attention being given to recommended protocols for their operation and management, for example, satisfactory experimental model designs; sample collection and laboratory processing techniques; the selection of sample-specific NMR pulse sequences for saliva analysis; and strategies available for the confirmation of resonance assignments for both endogenous and exogenous molecules in this biofluid. This article also features an original case study, which is focussed on the use of NMR-based salivary metabolomics techniques to provide some key biomarkers for the diagnosis of pharyngitis, and an example of how to 'police' such studies and to recognise participants who perceive that they actually have this disorder but do not from their metabolic profiles and multivariate analysis pattern-based clusterings. The biochemical and clinical significance of these multidimensional metabolomics investigations are discussed in detail.
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Targeted profiling of polar metabolites in cancer metabolic reprogramming by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2022; 1686:463654. [DOI: 10.1016/j.chroma.2022.463654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
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Bonicelli A, Cheung W, Hughes S, Wescott DJ, Procopio N. Preliminary Investigation of the Effect of Maceration Procedures on Bone Metabolome and Lipidome. Metabolites 2022; 12:1020. [PMID: 36355103 PMCID: PMC9693520 DOI: 10.3390/metabo12111020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
The study of post-mortem changes is a crucial component of forensic investigation. Human forensic taphonomic facilities (HFTFs) are the only institutions allowing the design and execution of controlled human decomposition experiments. When bodies are skeletonized, bones are normally stored in skeletal collections and used for anthropological studies. However, HFTFs apply chemical and/or thermal treatments to the remains prior bone long-term storage. These treatments are believed to alter heavily the original biochemical and molecular signature of bone material. The present study aims to evaluate the effect of these procedures on the bone metabolome and lipidome by using an animal bone model. Three intact bovine tibiae were processed using three protocols routinely applied at HFTFs, and their three counterparts were used as non-treated controls. Bone powder samples were subjected to biphasic extraction and both metabolites and lipids were analysed via liquid chromatography tandem mass-spectrometry. Results showed severe reductions in the abundances of both metabolites and lipids, and the presence of contamination introduced by cleaning agents. Despite the preliminary nature of the study, we demonstrated that the biochemical profile of bone is heavily affected by the maceration procedures. Ideally, these treatments should be avoided, or replaced by minimally invasive procedures agreed across HFTFs.
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Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX 773402525, USA
| | - Daniel J. Wescott
- Forensic Anthropology Center at Texas State, Department of Anthropology, Texas State University, San Marcos, TX 78666, USA
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
- Forensic Anthropology Center at Texas State, Department of Anthropology, Texas State University, San Marcos, TX 78666, USA
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Bindila L, Eid T, Mills JD, Hildebrand MS, Brennan GP, Masino SA, Whittemore V, Perucca P, Reid CA, Patel M, Wang KK, van Vliet EA. A companion to the preclinical common data elements for proteomics, lipidomics, and metabolomics data in rodent epilepsy models. A report of the TASK3-WG4 omics working group of the ILAE/AES joint translational TASK force. Epilepsia Open 2022. [PMID: 36259125 DOI: 10.1002/epi4.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/19/2022] [Indexed: 11/07/2022] Open
Abstract
The International League Against Epilepsy/American Epilepsy Society (ILAE/AES) Joint Translational Task Force established the TASK3 working groups to create common data elements (CDEs) for various preclinical epilepsy research disciplines. This is the second in a two-part series of omics papers, with the other including genomics, transcriptomics, and epigenomics. The aim of the CDEs was to improve the standardization of experimental designs across a range of epilepsy research-related methods. We have generated CDE tables with key parameters and case report forms (CRFs) containing the essential contents of the study protocols for proteomics, lipidomics, and metabolomics of samples from rodent models and people with epilepsy. We discuss the important elements that need to be considered for the proteomics, lipidomics, and metabolomics methodologies, providing a rationale for the parameters that should be documented.
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Affiliation(s)
- Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Tore Eid
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - James D Mills
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, the Netherlands
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Gary P Brennan
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Susan A Masino
- Neuroscience Program and Psychology Department, Life Sciences Center, Trinity College, Hartford, Connecticut, USA
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Piero Perucca
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Austin Health, Heidelberg, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Christopher A Reid
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Manisha Patel
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kevin K Wang
- Program for Neurotrauma, Neuroproteomics & Biomarker Research (NNBR), Department of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, Florida, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, Florida, USA
| | - Erwin A van Vliet
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, the Netherlands
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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Stability of Metabolomic Content during Sample Preparation: Blood and Brain Tissues. Metabolites 2022; 12:metabo12090811. [PMID: 36144215 PMCID: PMC9505456 DOI: 10.3390/metabo12090811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Thermal and enzymatic reactions can significantly change the tissue metabolomic content during the sample preparation. In this work, we evaluated the stability of metabolites in human whole blood, serum, and rat brain, as well as in metabolomic extracts from these tissues. We measured the concentrations of 63 metabolites in brain and 52 metabolites in blood. We have shown that metabolites in the extracts from biological tissues are stable within 24 h at 4 °C. Serum and whole blood metabolomes are also rather stable, changes in metabolomic content of the whole blood homogenate become apparent only after 1–2 h of incubation at 4 °C, and become strong after 24 h. The most significant changes correspond to energy metabolites: the concentrations of ATP and ADP decrease fivefold, and the concentrations of NAD, NADH, and NADPH decrease below the detectable level. A statistically significant increase was observed for AMP, IMP, hypoxanthine, and nicotinamide. The brain tissue is much more metabolically active than human blood, and significant metabolomic changes occur already within the first several minutes during the brain harvest and sample homogenization. At a longer timescale (hours), noticeable changes were observed for all classes of compounds, including amino acids, organic acids, alcohols, amines, sugars, nitrogenous bases, nucleotides, and nucleosides.
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Serum and Soleus Metabolomics Signature of Klf10 Knockout Mice to Identify Potential Biomarkers. Metabolites 2022; 12:metabo12060556. [PMID: 35736488 PMCID: PMC9231117 DOI: 10.3390/metabo12060556] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
The transcription factor Krüppel-like factor 10 (Klf10), also known as Tieg1 for TGFβ (Inducible Early Gene-1) is known to control numerous genes in many cell types that are involved in various key biological processes (differentiation, proliferation, apoptosis, inflammation), including cell metabolism and human disease. In skeletal muscle, particularly in the soleus, deletion of the Klf10 gene (Klf10 KO) resulted in ultrastructure fiber disorganization and mitochondrial metabolism deficiencies, characterized by muscular hypertrophy. To determine the metabolic profile related to loss of Klf10 expression, we analyzed blood and soleus tissue using UHPLC-Mass Spectrometry. Metabolomics analyses on both serum and soleus revealed profound differences between wild-type (WT) and KO animals. Klf10 deficient mice exhibited alterations in metabolites associated with energetic metabolism. Additionally, chemical classes of aromatic and amino-acid compounds were disrupted, together with Krebs cycle intermediates, lipids and phospholipids. From variable importance in projection (VIP) analyses, the Warburg effect, citric acid cycle, gluconeogenesis and transfer of acetyl groups into mitochondria appeared to be possible pathways involved in the metabolic alterations observed in Klf10 KO mice. These studies have revealed essential roles for Klf10 in regulating multiple metabolic pathways whose alterations may underlie the observed skeletal muscle defects as well as other diseases.
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Lanznaster D, Bruno C, Bourgeais J, Emond P, Zemmoura I, Lefèvre A, Reynier P, Eymieux S, Blanchard E, Vourc’h P, Andres CR, Bakkouche SE, Herault O, Favard L, Corcia P, Blasco H. Metabolic Profile and Pathological Alterations in the Muscle of Patients with Early-Stage Amyotrophic Lateral Sclerosis. Biomedicines 2022; 10:biomedicines10061307. [PMID: 35740329 PMCID: PMC9220134 DOI: 10.3390/biomedicines10061307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 12/26/2022] Open
Abstract
Diverse biomarkers and pathological alterations have been found in muscle of patients with Amyotrophic lateral sclerosis (ALS), but the relation between such alterations and dysfunction in energetic metabolism remains to be investigated. We established the metabolome of muscle and serum of ALS patients and correlated these findings with the clinical status and pathological alterations observed in the muscle. We obtained data from 20 controls and 17 ALS patients (disease duration: 9.4 ± 6.8 months). Multivariate metabolomics analysis identified a distinct serum metabolome for ALS compared to controls (p-CV-ANOVA < 0.035) and revealed an excellent discriminant profile for muscle metabolome (p-CV-ANOVA < 0.0012). Citramalate was discriminant for both muscle and serum. High lauroylcarnitine levels in muscle were associated with low Forced Vital Capacity. Transcriptomics analysis of key antioxidant enzymes showed an upregulation of SOD3 (p = 0.0017) and GLRX2(1) (p = 0.0022) in ALS muscle. Analysis of mitochondrial enzymatic activity in muscle revealed higher complex II/CS (p = 0.04) and lower LDH (p = 0.03) activity in ALS than in controls. Our study showed, for the first time, a global dysfunction in the muscle of early-stage ALS patients. Furthermore, we identified novel metabolites to be employed as biomarkers for diagnosis and prognosis of ALS patients.
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Affiliation(s)
- Débora Lanznaster
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Correspondence:
| | - Clément Bruno
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
| | - Jérôme Bourgeais
- CNRS ERL7001, EA 7501 GICC, Université de Tours, 37000 Tours, France; (J.B.); (O.H.)
| | - Patrick Emond
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Médecine Nucléaire In Vitro, CHU de Tours, 37000 Tours, France
| | - Ilyess Zemmoura
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Neurochirurgie, CHU de Tours, 37000 Tours, France
| | - Antoine Lefèvre
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
| | - Pascal Reynier
- Service de Biochimie et Biologie Moléculaire, CHU d’Angers, 49000 Angers, France;
- Mitovasc-Mitolab, UMR CNRS6015-INSERM1083, 49000 Angers, France
| | - Sébastien Eymieux
- Plateforme IBiSA de Microscopie Electronique, Université de Tours et CHU de Tours, 37000 Tours, France; (S.E.); (E.B.)
- INSERM U1259, Université de Tours, 37000 Tours, France
| | - Emmanuelle Blanchard
- Plateforme IBiSA de Microscopie Electronique, Université de Tours et CHU de Tours, 37000 Tours, France; (S.E.); (E.B.)
- INSERM U1259, Université de Tours, 37000 Tours, France
| | - Patrick Vourc’h
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
| | - Christian R. Andres
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
| | | | - Olivier Herault
- CNRS ERL7001, EA 7501 GICC, Université de Tours, 37000 Tours, France; (J.B.); (O.H.)
| | - Luc Favard
- Service de Neurologie, CHU de Tours, 37000 Tours, France;
| | - Philippe Corcia
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Neurologie, CHU de Tours, 37000 Tours, France;
| | - Hélène Blasco
- UMR 1253, iBrain, Université de Tours, INSERM, 37000 Tours, France; (C.B.); (P.E.); (I.Z.); (A.L.); (P.V.); (C.R.A.); (P.C.); (H.B.)
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, 37000 Tours, France
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Boeri L, Donnaloja F, Campanile M, Sardelli L, Tunesi M, Fusco F, Giordano C, Albani D. Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy. Neurobiol Dis 2022; 164:105614. [PMID: 35017031 DOI: 10.1016/j.nbd.2022.105614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.
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Affiliation(s)
- Lucia Boeri
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Francesca Donnaloja
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marzia Campanile
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marta Tunesi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Federica Fusco
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milan, Italy.
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Defining Blood Plasma and Serum Metabolome by GC-MS. Metabolites 2021; 12:metabo12010015. [PMID: 35050137 PMCID: PMC8779220 DOI: 10.3390/metabo12010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.
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Analytical Methodology for a Metabolome Atlas of Goat's Plasma, Milk and Feces Using 1H-NMR and UHPLC-HRMS. Metabolites 2021; 11:metabo11100681. [PMID: 34677396 PMCID: PMC8537934 DOI: 10.3390/metabo11100681] [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: 08/31/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022] Open
Abstract
Metabolomics has been increasingly used in animal and food sciences. Animal health is one of the most important factor that can also alter animal integrity and welfare. Some studies have already investigated the link between health and metabolic profile of dairy animals. These studies in metabolomics often consider a single type of sample using a single analytical platform (nuclear magnetic resonance or mass spectrometry). Only few studies with multi-platform approaches are also used with a single or a multi type of sample, but they mainly consider dairy cows’ metabolome although dairy goats present similar diseases, that it could be interesting to detect early to preserve animal health and milk production. This study aims to create a metabolic atlas of goat plasma, milk and feces, based on healthy animals. Our study describes a standard operating procedure for three goat matrices: blood plasma, milk, and feces using multiple platforms (NMR (1H), UHPLC (RP)-MS and UHPLC (HILIC)-MS) that follows a unique sample preparation procedure for each sample type to be analyzed on multi-platforms basis. Our method was evaluated for its robustness and allowed a better characterization of goat metabolic profile in healthy conditions.
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