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Vanden Broecke E, Van Mulders L, De Paepe E, Daminet S, Vanhaecke L. Optimization and validation of metabolomics methods for feline urine and serum towards application in veterinary medicine. Anal Chim Acta 2024; 1310:342694. [PMID: 38811133 DOI: 10.1016/j.aca.2024.342694] [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: 12/07/2023] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Metabolomics is an emerging and powerful technology that offers a comprehensive view of an organism's physiological status. Although widely applied in human medicine, it is only recently making its introduction in veterinary medicine. As a result, validated metabolomics protocols in feline medicine are lacking at the moment. Since biological interpretation of metabolomics data can be misled by the extraction method used, species and matrix-specific optimized and validated metabolomic protocols are sorely needed. RESULTS Systematic optimization was performed using fractional factorial experiments for both serum (n = 57) and urine (n = 24), evaluating dilution for both matrices, and aliquot and solvent volume, protein precipitation time and temperature for serum. For the targeted (n = 76) and untargeted (n = 1949) validation of serum respectively, excellent instrumental, intra-assay and inter-day precision were observed (CV ≤ 15% or 30%, respectively). Linearity deemed sufficient both targeted and untargeted (R2 ≥ 0.99 or 0.90, respectively). An appropriate targeted recovery between 70 and 130% was achieved. For the targeted (n = 69) and untargeted (n = 2348) validation of the urinary protocol, excellent instrumental and intra-assay precision were obtained (CV ≤ 15% or 30%, respectively). Subsequently, the discriminative ability of our metabolomics methods was confirmed for feline chronic kidney disease (CKD) by univariate statistics (n = 41 significant metabolites for serum, and n = 55 for urine, p-value<0.05) and validated OPLS-DA models (R2(Y) > 0.95, Q2(Y) > 0.65, p-value<0.001 for both matrices). SIGNIFICANCE This study is the first to present an optimized and validated wholistic metabolomics methods for feline serum and urine using ultra-high performance liquid chromatography coupled to quadrupole-Orbitrap high-resolution mass spectrometry. This robust methodology opens avenues for biomarker panel selection and a deeper understanding of feline CKD pathophysiology and other feline applications.
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Affiliation(s)
- Ellen Vanden Broecke
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium; Ghent University, Faculty of Veterinary Medicine, Department of Small Animals, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Laurens Van Mulders
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium; Ghent University, Faculty of Veterinary Medicine, Department of Small Animals, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Ellen De Paepe
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Sylvie Daminet
- Ghent University, Faculty of Veterinary Medicine, Department of Small Animals, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium; Queen's University Belfast, School of Biological Sciences, Institute for Global Food Security, Chlorine Gardens 19, BT9-5DL, Belfast, Northern Ireland, United Kingdom.
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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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Wang F, Mai J, Wang H, Xu Y, Zhou X, Xie Z, Yu B, Liu P, Liu W, Cheng Y. Identification of Erzhu Jiedu Recipe and its molecular mechanism underlying inhibited human hepatoma cells by UHPLC-Q-Exactive Orbitrap HRMS and network pharmacology. JOURNAL OF ETHNOPHARMACOLOGY 2024; 325:117893. [PMID: 38336184 DOI: 10.1016/j.jep.2024.117893] [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: 12/06/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Erzhu Jiedu Recipe (EZJDR) is a formula of traditional Chinese medicine (TCM) for treating hepatitis B virus-related hepatocellular carcinoma (HBV-HCC). However, its effective components and the mechanism of action remain unclear. AIM OF THE STUDY To explain how the active compounds of EZJDR suppress the growth of hepatoma cells. METHODS UHPLC-Q-Exactive Orbitrap HRMS was used to identify the chemical constituents of EZJDR and their distribution in the serum and liver of mice. Together with experimental investigations, network pharmacology unraveled the molecular mechanism of components of EZJDR underlying the inhibited Hep3B cells. RESULTS A total of 138 compounds which can be divided into 18 kinds of components (such as sesquiterpenoids, diterpenoids, anthraquinones, flavonoids and so on) were found in the aqueous extract of EZJDR. Of these components, the tricyclic-diterpenoids exhibited a highest exposure in the serum (74.5%) and liver (94.7%) of mice. The network pharmacology revealed that multiple components of EZJDR interacted with key node genes involved in apoptosis, proliferation, migration and metabolism through various signaling pathways, including ligand binding and protein phosphorylation. In vitro experiments demonstrated that 6 tricyclic-diterpenoids, 2 anthraquinones and 1 flavonoid inhibited the viability of Hep3B cells, with IC50 values ranging from 3.81 μM to 37.72 μM. Dihydrotanshinone I had the most potent bioactivity, arresting the S phase of cell cycle and inducing apoptosis. This compound changed the expression of proteins, including Bad, Bax, Bcl-2, Bal-x, caspase3 and catalase, which were associated with mitochondria-mediated apoptotic pathways. Moreover, dihydrotanshinone I increased the levels of p21 proteins, but decreased the phosphorylated p53, suggesting accumulation of p53 protein prevented cell cycle progression of Hep3B cells with damaged DNA. CONCLUSIONS These results suggested that multiple components of EZJDR-diterpenoid, anthraquinone and flavonoid-could be the effective material for the treatment of HBV-HCC. This research provided valuable insights into the molecular mechanism of action underlying the therapeutic effects of EZJDR.
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Affiliation(s)
- Fangyuan Wang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jingyin Mai
- Emergency Department, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Haoyi Wang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ying Xu
- Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, School of Traditional Chinese Medicine, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xianglu Zhou
- Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, School of Traditional Chinese Medicine, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhishen Xie
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Bao Yu
- College of Traditional Chinese Medicine, Chongqing College of Traditional Chinese Medicine, Chongqing, 402760, China
| | - Ping Liu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Wei Liu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Department of Pharmacy, The SATCM Third Grade Laboratory of Traditional Chinese Medicine Preparations, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, School of Traditional Chinese Medicine, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Yang Cheng
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Cafarella C, Mangraviti D, Rigano F, Dugo P, Mondello L. Rapid evaporative ionization mass spectrometry: A survey through 15 years of applications. J Sep Sci 2024; 47:e2400155. [PMID: 38772742 DOI: 10.1002/jssc.202400155] [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: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
Rapid evaporative ionization mass spectrometry (REIMS) is a relatively recent MS technique explored in many application fields, demonstrating high versatility in the detection of a wide range of chemicals, from small molecules (phenols, amino acids, di- and tripeptides, organic acids, and sugars) to larger biomolecules, that is, phospholipids and triacylglycerols. Different sampling devices were used depending on the analyzed matrix (liquid or solid), resulting in distinct performances in terms of automation, reproducibility, and sensitivity. The absence of laborious and time-consuming sample preparation procedures and chromatographic separations was highlighted as a major advantage compared to chromatographic methods. REIMS was successfully used to achieve a comprehensive sample profiling according to a metabolomics untargeted analysis. Moreover, when a multitude of samples were available, the combination with chemometrics allowed rapid sample differentiation and the identification of discriminant features. The present review aims to provide a survey of literature reports based on the use of such analytical technology, highlighting its mode of operation in different application areas, ranging from clinical research, mostly focused on cancer diagnosis for the accurate identification of tumor margins, to the agri-food sector aiming at the safeguard of food quality and security.
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Affiliation(s)
- Cinzia Cafarella
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
| | - Domenica Mangraviti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
| | - Francesca Rigano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
| | - Paola Dugo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Chromaleont s.r.l., former Veterinary School, University of Messina, Messina, Italy
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Messina Institute of Technology, former Veterinary School, University of Messina, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Chromaleont s.r.l., former Veterinary School, University of Messina, Messina, Italy
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Pedraz-Petrozzi B, Lamadé EK, Marszalek-Grabska M, Trzpil A, Lindner O, Meininger P, Fornal E, Turski WA, Witt SH, Gilles M, Deuschle M. Fetal Sex as Moderating Factor for the Relationship Between Maternal Childhood Trauma and Salivary Kynurenic Acid and Tryptophan in Pregnancy: A Pilot Study. Int J Tryptophan Res 2024; 17:11786469241244603. [PMID: 38660592 PMCID: PMC11041113 DOI: 10.1177/11786469241244603] [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: 08/24/2023] [Accepted: 03/17/2024] [Indexed: 04/26/2024] Open
Abstract
Traumatic experiences and fetal development influence tryptophan (TRP) and its neuroactive byproduct, kynurenic acid (KYNA). Maternal TRP metabolite levels during pregnancy vary by fetal sex, with higher concentrations in mothers carrying male fetuses. This pilot study aimed to explore the relationship between offspring sex, maternal childhood trauma, and maternal salivary KYNA and TRP levels during pregnancy. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine KYNA and TRP levels in maternal saliva samples collected from 35 late-pregnancy participants. Maternal childhood trauma was assessed using the Childhood Trauma Questionnaire, including subscales for emotional abuse, physical abuse, sexual abuse, emotional neglect, and physical neglect. Among mothers pregnant with boys, salivary KYNA significantly correlated with physical and emotional neglect, and salivary TRP with emotional neglect. No significant correlations were found in mothers who delivered female offspring. Significant associations of childhood trauma and offspring sex were found for salivary KYNA but not TRP concentrations. Mothers with higher trauma levels who delivered boys exhibited higher levels of salivary KYNA compared to those with lower trauma levels. Moreover, mothers with higher trauma levels who delivered boys had higher salivary KYNA levels than those with higher trauma levels who delivered girls. This pilot study provides evidence of an association between maternal childhood trauma and TRP metabolism, measured in saliva, especially in mothers pregnant with boys. However, longitudinal studies with larger sample sizes are required to confirm these results.
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Affiliation(s)
- Bruno Pedraz-Petrozzi
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Eva Kathrin Lamadé
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Germany
| | | | - Alicja Trzpil
- Department of Bioanalytics, Medical University of Lublin, Poland
| | - Ole Lindner
- Center for Child and Adolescent Health, Pediatrics, University Hospital of Freiburg, Germany
| | - Pascal Meininger
- Department of Gynecology and Obstetrics, Westpfalz-Klinikum, Kaiserslautern, Germany
| | - Emilia Fornal
- Department of Bioanalytics, Medical University of Lublin, Poland
| | - Waldemar A Turski
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Poland
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Maria Gilles
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Michael Deuschle
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Germany
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Bradley R, Simon D, Spiga L, Xiang Y, Takats Z, Williams H. Laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS) demonstrates a direct impact of hypochlorous acid stress on PQS-mediated quorum sensing in Pseudomonas aeruginosa. mSystems 2024; 9:e0116523. [PMID: 38530056 PMCID: PMC11019781 DOI: 10.1128/msystems.01165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
To establish infections in human hosts, Pseudomonas aeruginosa must overcome innate immune-generated oxidative stress, such as the hypochlorous acid (HOCl) produced by neutrophils. We set out to find specific biomarkers of oxidative stress through the development of a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionization technique for mass spectrometry, laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS). We demonstrated the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100% accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrated that HOCl stress impacted the Pseudomonas quinolone signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were reduced by more than 75% in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors. IMPORTANCE This work demonstrates that a high-throughput ambient ionization mass spectrometry method can be used successfully to study a bacterial stress response. Its application to the opportunistic pathogen Pseudomonas aeruginosa led to the identification of specific oxidative stress biomarkers, and demonstrated that hypochlorous acid, an oxidant specifically produced by human neutrophils during infection, affects quorum sensing and reduces production of the virulence factors pyocyanin and elastase. No pyocyanin was detectable and elastase levels were reduced by more than 75% in bacteria grown in the presence of hypochlorous acid. This approach has the potential to be widely applicable to the characterization of the stress responses of bacteria.
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Affiliation(s)
- Rob Bradley
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Daniel Simon
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
- The Rosalind Franklin Institute, Didcot, United Kingdom
| | - Livia Spiga
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Yuchen Xiang
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Huw Williams
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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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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Siani-Rose M, McKee R, Cox S, Goldstein B, Abrams D, Taylor M, Kurek I. The Potential of Salivary Lipid-Based Cannabis-Responsive Biomarkers to Evaluate Medical Cannabis Treatment in Children with Autism Spectrum Disorder. Cannabis Cannabinoid Res 2023; 8:642-656. [PMID: 35343818 DOI: 10.1089/can.2021.0224] [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: 11/12/2022] Open
Abstract
Introduction: Autism spectrum disorder (ASD) is a group of heterogeneous neurodevelopmental conditions affecting social communication and social interaction. Medical cannabis (MC) treatment shows promising results as an approach to reduce behavioral difficulties, as determined mainly by subjective observations. We have recently shown the potential of cannabis-responsive biomarkers detected in saliva of children with ASD to objectively quantify the impact of successful MC treatment using a metabolomics approach. Since the pathology of ASD is associated with abnormal lipid metabolism, we used lipidomics on the same samples to (1) expand the repertoire of cannabis-responsive biomarkers and (2) provide preliminary insight into the role of MC on lipid metabolism. Materials and Methods: Saliva samples collected from children with ASD (n=15) treated with MC (both before and at the time of maximal impact of treatment) and an age-matched group of typically developing (TD) children (n=9) were subjected to untargeted lipidomics. The study was observational. Each child from the ASD group was receiving a unique individualized MC treatment regimen using off-the-shelf products as permitted by California law under physician supervision for at least 1 year. Doses of tetrahydrocannabinol (THC) ranged from 0.05 to 50 mg and cannabidiol (CBD) from 7.5 to 200 mg per treatment. The ASD group was evaluated for signs of improvement using parental brief Likert scale surveys. Results: Twenty-two potential lipid-based cannabis-responsive biomarkers exhibiting a shift toward the TD physiological levels in children with ASD after MC treatment were identified. Members from all five lipid subclasses known to be present in saliva were characterized. Preliminary lipid association network analysis suggests involvement of two subnetworks previously linked to (1) inflammation and/or redox regulation and (2) oxidative stress. The significant changes in sphingomyelin in this study and in N-acetyl-aspartate (NAA) previously detected in the metabolomics analysis of the same saliva samples may indicate a role of MC in neuron function. Conclusions: Our findings suggest that lipid metabolites in saliva can potentially serve as cannabis-responsive biomarkers and objectively quantify the impact of MC treatment, and indicate a possible mechanism of action for MC. This preliminary study requires further investigation with a larger population and appropriate clinical trial monitoring.
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Affiliation(s)
| | - Robert McKee
- Cannformatics, Inc., San Francisco, California, USA
| | - Stephany Cox
- Cannformatics, Inc., San Francisco, California, USA
| | | | | | | | - Itzhak Kurek
- Cannformatics, Inc., San Francisco, California, USA
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9
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De Spiegeleer M, Plekhova V, Geltmeyer J, Schoolaert E, Pomian B, Singh V, Wijnant K, De Windt K, Paukku V, De Loof A, Gies I, Michels N, De Henauw S, De Graeve M, De Clerck K, Vanhaecke L. Point-of-care applicable metabotyping using biofluid-specific electrospun MetaSAMPs directly amenable to ambient LA-REIMS. SCIENCE ADVANCES 2023; 9:eade9933. [PMID: 37294759 PMCID: PMC10256167 DOI: 10.1126/sciadv.ade9933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/05/2023] [Indexed: 06/11/2023]
Abstract
In recent years, ambient ionization mass spectrometry (AIMS) including laser ablation rapid evaporation IMS, has enabled direct biofluid metabolome analysis. AIMS procedures are, however, still hampered by both analytical, i.e., matrix effects, and practical, i.e., sample transport stability, drawbacks that impede metabolome coverage. In this study, we aimed at developing biofluid-specific metabolome sampling membranes (MetaSAMPs) that offer a directly applicable and stabilizing substrate for AIMS. Customized rectal, salivary, and urinary MetaSAMPs consisting of electrospun (nano)fibrous membranes of blended hydrophilic (polyvinylpyrrolidone and polyacrylonitrile) and lipophilic (polystyrene) polymers supported metabolite absorption, adsorption, and desorption. Moreover, MetaSAMP demonstrated superior metabolome coverage and transport stability compared to crude biofluid analysis and was successfully validated in two pediatric cohorts (MetaBEAse, n = 234 and OPERA, n = 101). By integrating anthropometric and (patho)physiological with MetaSAMP-AIMS metabolome data, we obtained substantial weight-driven predictions and clinical correlations. In conclusion, MetaSAMP holds great clinical application potential for on-the-spot metabolic health stratification.
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Affiliation(s)
- Margot De Spiegeleer
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Vera Plekhova
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Jozefien Geltmeyer
- Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Ella Schoolaert
- Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Beata Pomian
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Varoon Singh
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Kathleen Wijnant
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Kimberly De Windt
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Volter Paukku
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Alexander De Loof
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Inge Gies
- Department of Pediatrics, Free University of Brussels (VUB), University Hospital Brussels (UZ Brussel), Brussels, Belgium
| | - Nathalie Michels
- Department of Developmental, Personality and Social Psychology, Ghent University, Ghent, Belgium
| | - Stefaan De Henauw
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Marilyn De Graeve
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Karen De Clerck
- Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast, UK
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10
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Nam M, Jo SR, Park JH, Kim MS. Evaluation of critical factors in the preparation of saliva sample from healthy subjects for metabolomics. J Pharm Biomed Anal 2022; 223:115145. [DOI: 10.1016/j.jpba.2022.115145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
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11
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Zhou J, Li J, Gao W, Zhang S, Wang C, Lin J, Zhang S, Yu J, Tang K. Combination of continuous wavelet transform and genetic algorithm-based Otsu for efficient mass spectrometry peak detection. Biochem Biophys Res Commun 2022; 624:75-80. [PMID: 35940130 DOI: 10.1016/j.bbrc.2022.07.083] [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: 07/16/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/28/2022]
Abstract
Mass spectrometry (MS) data is susceptible to random noises and alternating baseline, posing great challenges to spectral peak detection, especially for weak peaks and overlapping peaks. Herein, an efficient peak detection algorithm combining continuous wavelet transform (CWT) and genetic algorithm-based threshold segmentation (denoted as WSTGA) for mass spectrometry was proposed. Firstly, Mexican Hat wavelet was selected as the mother wavelet by comparing the matching degree between the difference of Gaussian (DOG) and different wavelets. Subsequently, the ridges and valleys were identified from 2D wavelet coefficient matrix. Afterward, an improved threshold segmentation method, Otsu method based on genetic algorithm, was introduced to find optimal segmentation threshold and achieve better image segmentation, overcoming the deficiency of traditional Otsu method that cannot handle long-tailed unimodal histograms. Finally, the characteristic peaks were successfully identified by utilizing the ridge-valley lines in wavelet space and original spectrum. Receiver operating characteristic (ROC) curve, area under curve (AUC) and F₁ measure are used as criterions to evaluate performance of peak detection algorithms. Compared with multi-scale peak detection (MSPD) and CWT and image segmentation (CWT-IS) methods, all the results showed that WSTGA can achieve better peak detection. More importantly, the experimental results from MALDI-TOF spectra demonstrated that WSTGA can effectively detect more weak peaks and overlapping peaks while maintaining a lower false peak detection rate than MSPD and CWT-IS methods, indicating its great advantages in characteristic peak identification.
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Affiliation(s)
- Junfei Zhou
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, PR China; Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, PR China
| | - Junhui Li
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, PR China; Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, PR China
| | - Wenqing Gao
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, PR China.
| | - Shun Zhang
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, PR China; Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, 2019E10020, Ningbo, PR China
| | - Chenlu Wang
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, PR China
| | - Jing Lin
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, PR China; Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, 2019E10020, Ningbo, PR China
| | - Sijia Zhang
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, PR China; Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, 2019E10020, Ningbo, PR China
| | - Jiancheng Yu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, PR China; Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, PR China.
| | - Keqi Tang
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, PR China.
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12
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Challen B, Cramer R. Advances in ionisation techniques for mass spectrometry-based omics research. Proteomics 2022; 22:e2100394. [PMID: 35709387 DOI: 10.1002/pmic.202100394] [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: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022]
Abstract
Omics analysis by mass spectrometry (MS) is a vast field, with proteomics, metabolomics and lipidomics dominating recent research by exploiting biological MS ionisation techniques. Traditional MS ionisation techniques such as electrospray ionisation have limitations in analyte-specific sensitivity, modes of sampling and throughput, leading to many researchers investigating new ionisation methods for omics research. In this review, we examine the current landscape of these new ionisation techniques, divided into the three groups of (electro)spray-based, laser-based and other miscellaneous ionisation techniques. Due to the wide range of new developments, this review can only provide a starting point for further reading on each ionisation technique, as each have unique benefits, often for specialised applications, which promise beneficial results for different areas in the omics world.
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Affiliation(s)
- Bob Challen
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
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13
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Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part I: Emerging Platforms and Perspectives. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
1H NMR-based metabolomics analysis of human saliva, other oral fluids, and/or tissue biopsies serves as a valuable technique for the exploration of metabolic processes, and when associated with ’state-of-the-art’ multivariate (MV) statistical analysis strategies, provides a powerful means of examining the identification of characteristic metabolite patterns, which may serve to differentiate between patients with oral health conditions (e.g., periodontitis, dental caries, and oral cancers) and age-matched heathy controls. This approach may also be employed to explore such discriminatory signatures in the salivary 1H NMR profiles of patients with systemic diseases, and to date, these have included diabetes, Sjörgen’s syndrome, cancers, neurological conditions such as Alzheimer’s disease, and viral infections. However, such investigations are complicated in view of quite a large number of serious inconsistencies between the different studies performed by independent research groups globally; these include differing protocols and routes for saliva sample collection (e.g., stimulated versus unstimulated samples), their timings (particularly the oral activity abstention period involved, which may range from one to 12 h or more), and methods for sample transport, storage, and preparation for NMR analysis, not to mention a very wide variety of demographic variables that may influence salivary metabolite concentrations, notably the age, gender, ethnic origin, salivary flow-rate, lifestyles, diets, and smoking status of participant donors, together with their exposure to any other possible convoluting environmental factors. In view of the explosive increase in reported salivary metabolomics investigations, in this update, we critically review a wide range of critical considerations for the successful performance of such experiments. These include the nature, composite sources, and biomolecular status of human saliva samples; the merits of these samples as media for the screening of disease biomarkers, notably their facile, unsupervised collection; and the different classes of such metabolomics investigations possible. Also encompassed is an account of the history of NMR-based salivary metabolomics; our recommended regimens for the collection, transport, and storage of saliva samples, along with their preparation for NMR analysis; frequently employed pulse sequences for the NMR analysis of these samples; the supreme resonance assignment benefits offered by homo- and heteronuclear two-dimensional NMR techniques; deliberations regarding salivary biomolecule quantification approaches employed for such studies, including the preprocessing and bucketing of multianalyte salivary NMR spectra, and the normalization, transformation, and scaling of datasets therefrom; salivary phenotype analysis, featuring the segregation of a range of different metabolites into ‘pools’ grouped according to their potential physiological sources; and lastly, future prospects afforded by the applications of LF benchtop NMR spectrometers for direct evaluations of the oral or systemic health status of patients at clinical ‘point-of-contact’ sites, e.g., dental surgeries. This commentary is then concluded with appropriate recommendations for the conduct of future salivary metabolomics studies. Also included are two original case studies featuring investigations of (1) the 1H NMR resonance line-widths of selected biomolecules and their possible dependence on biomacromolecular binding equilibria, and (2) the combined univariate (UV) and MV analysis of saliva specimens collected from a large group of healthy control participants in order to potentially delineate the possible origins of biomolecules therein, particularly host- versus oral microbiome-derived sources. In a follow-up publication, Part II of this series, we conduct censorious reviews of reported observations acquired from a diversity of salivary metabolomics investigations performed to evaluate both localized oral and non-oral diseases. Perplexing problems encountered with these again include those arising from sample collection and preparation protocols, along with 1H NMR spectral misassignments.
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14
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Nauta S, Huysmans P, Tuijthof GM, Eijkel GB, Poeze M, Siegel TP, Heeren RMA. Automated 3D Sampling and Imaging of Uneven Sample Surfaces with LA-REIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:111-122. [PMID: 34882413 PMCID: PMC8739836 DOI: 10.1021/jasms.1c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The analysis of samples with large height variations remains a challenge for mass spectrometry imaging (MSI), despite many technological advantages. Ambient sampling and ionization MS techniques allow for the molecular analysis of sample surfaces with height variations, but most techniques lack MSI capabilities. We developed a 3D MS scanner for the automated sampling and imaging of a 3D surface with laser-assisted rapid evaporative ionization mass spectrometry (LA-REIMS). The sample is moved automatically with a constant distance between the laser probe and sample surface in the 3D MS Scanner. The topography of the surface was scanned with a laser point distance sensor to define the MS measurement points. MS acquisition was performed with LA-REIMS using a surgical CO2 laser coupled to a qTOF instrument. The topographical scan and MS acquisition can be completed within 1 h using the 3D MS scanner for 300 measurement points on uneven samples with a spatial resolution of 2 mm in the top view, corresponding to 22.04 cm2. Comparison between the automated acquisition with the 3D MS scanner and manual acquisition by hand showed that the automation resulted in increased reproducibility between the measurement points. 3D visualizations of molecular distributions related to structural differences were shown for an apple, a marrowbone, and a human femoral head to demonstrate the imaging feasibility of the system. The developed 3D MS scanner allows for the automated sampling of surfaces with uneven topographies with LA-REIMS, which can be used for the 3D visualization of molecular distributions of these surfaces.
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Affiliation(s)
- Sylvia
P. Nauta
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
- Department
of Orthopedic Surgery and Trauma Surgery, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
| | - Pascal Huysmans
- Research
Engineering, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Gabriëlle
J. M. Tuijthof
- Research
Engineering, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Gert B. Eijkel
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Martijn Poeze
- Department
of Surgery, Division of Trauma Surgery, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
- NUTRIM,
School for Nutrition and Translational Research in Metabolism, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
| | - Tiffany Porta Siegel
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Ron M. A. Heeren
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
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15
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De Spiegeleer M, De Paepe E, Van Meulebroek L, Gies I, De Schepper J, Vanhaecke L. Paediatric obesity: a systematic review and pathway mapping of metabolic alterations underlying early disease processes. Mol Med 2021; 27:145. [PMID: 34742239 PMCID: PMC8571978 DOI: 10.1186/s10020-021-00394-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The alarming trend of paediatric obesity deserves our greatest awareness to hinder the early onset of metabolic complications impacting growth and functionality. Presently, insight into molecular mechanisms of childhood obesity and associated metabolic comorbidities is limited. This systematic review aimed at scrutinising what has been reported on putative metabolites distinctive for metabolic abnormalities manifesting at young age by searching three literature databases (Web of Science, Pubmed and EMBASE) during the last 6 years (January 2015-January 2021). Global metabolomic profiling of paediatric obesity was performed (multiple biological matrices: blood, urine, saliva and adipose tissue) to enable overarching pathway analysis and network mapping. Among 2792 screened Q1 articles, 40 met the eligibility criteria and were included to build a database on metabolite markers involved in the spectrum of childhood obesity. Differential alterations in multiple pathways linked to lipid, carbohydrate and amino acid metabolisms were observed. High levels of lactate, pyruvate, alanine and acetate marked a pronounced shift towards hypoxic conditions in children with obesity, and, together with distinct alterations in lipid metabolism, pointed towards dysbiosis and immunometabolism occurring early in life. Additionally, aberrant levels of several amino acids, most notably belonging to tryptophan metabolism including the kynurenine pathway and its relation to histidine, phenylalanine and purine metabolism were displayed. Moreover, branched-chain amino acids were linked to lipid, carbohydrate, amino acid and microbial metabolism, inferring a key role in obesity-associated insulin resistance. CONCLUSIONS This systematic review revealed that the main metabolites at the crossroad of dysregulated metabolic pathways underlying childhood obesity could be tracked down to one central disturbance, i.e. impending insulin resistance for which reference values and standardised measures still are lacking. In essence, glycolytic metabolism was evinced as driving energy source, coupled to impaired Krebs cycle flux and ß-oxidation. Applying metabolomics enabled to retrieve distinct metabolite alterations in childhood obesity(-related insulin resistance) and associated pathways at early age and thus could provide a timely indication of risk by elucidating early-stage biomarkers as hallmarks of future metabolically unhealthy phenotypes.
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Affiliation(s)
- Margot De Spiegeleer
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Ellen De Paepe
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Inge Gies
- KidZ Health Castle, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090, Brussel, Belgium
| | - Jean De Schepper
- KidZ Health Castle, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090, Brussel, Belgium.,Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium. .,Institute for Global Food Security, School of Biological Sciences, Queen's University, University Road, Belfast, BT7 1NN, UK.
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16
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De Vrieze J, Heyer R, Props R, Van Meulebroek L, Gille K, Vanhaecke L, Benndorf D, Boon N. Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles. WATER RESEARCH 2021; 202:117422. [PMID: 34280807 DOI: 10.1016/j.watres.2021.117422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium; Division of Soil and Water Management, Department of Earth and Environmental sciences, KU Leuven, Kasteelpark Arenberg 20, PO box 2411, B-3001, Leuven, Belgium; Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, PO box 2424, B-3001, Leuven, Belgium.
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Karen Gille
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany; Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354, Köthen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
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17
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Plekhova V, Van Meulebroek L, De Graeve M, Perdones-Montero A, De Spiegeleer M, De Paepe E, Van de Walle E, Takats Z, Cameron SJS, Vanhaecke L. Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry. Nat Protoc 2021; 16:4327-4354. [PMID: 34341579 DOI: 10.1038/s41596-021-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/31/2021] [Indexed: 01/29/2023]
Abstract
Of the many metabolites involved in any clinical condition, only a narrow range of biomarkers is currently being used in the clinical setting. A key to personalized medicine would be to extend this range. Metabolic fingerprinting provides a more comprehensive insight, but many methods used for metabolomics analysis are too complex and time-consuming to be diagnostically useful. Here, a rapid evaporative ionization mass spectrometry (REIMS) system for direct ex vivo real-time analysis of biofluids with minor sample pretreatment is detailed. The REIMS can be linked to various laser wavelength systems (such as optical parametric oscillator or CO2 laser) and with automation for high-throughput analysis. Laser-induced sample evaporation occurs within seconds through radiative heating with the plume guided to the MS instrument. The presented procedure includes (i) laser setup with automation, (ii) analysis of biofluids (blood/urine/stool/saliva/sputum/breast milk) and (iii) data analysis. We provide the optimal settings for biofluid analysis and quality control, enabling sensitive, precise and robust analysis. Using the automated setup, 96 samples can be analyzed in ~35-40 min per ionization mode, with no intervention required. Metabolic fingerprints are made up of 2,000-4,000 features, for which relative quantification can be achieved at high repeatability when total ion current normalization is applied. With saliva and feces as example matrices, >70% of features had a coefficient of variance ≤30%. However, to achieve acceptable long-term reproducibility, additional normalizations by, e.g., LOESS are recommended, especially for positive ionization.
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Affiliation(s)
- Vera Plekhova
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium.,ProDigest BV, Zwijnaarde, Belgium
| | - Marilyn De Graeve
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | | | | | - Ellen De Paepe
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Emma Van de Walle
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Zoltan Takats
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Simon J S Cameron
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium. .,School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK.
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18
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Ma B, Lou T, Wang T, Li R, Liu J, Yu S, Guo Y, Wang Z, Wang J. Comprehensive metabolism study of swertiamarin in rats using ultra high-performance liquid chromatography coupled with Quadrupole-Exactive Orbitrap mass spectrometry. Xenobiotica 2021; 51:455-466. [PMID: 33356745 DOI: 10.1080/00498254.2020.1869856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Swertiamarin, a natural ingredient with potent pharmacological activities in the iridoid glycoside family, had been reported to have significant therapeutic effects on a variety of human diseases.In this study, a systematic and efficient strategy based on UHPLC-Q-Exactive Orbitrap mass spectrometry was established to reveal the metabolic profile of swertiamarin in rat urine, plasma, and faeces.First of all, post-acquisition data-mining methods, including multiple mass defect filters (MMDFs) and high-resolution extracted ion chromatograms (HREICs), were developed to screen the metabolite candidates of swertiamarin from the complete mass scan data sets.Second, according to the diagnostic product ions (DPIs), neutral loss fragments (NLFs), chromatographic retention time, accurate mass measurement and calculated Clog P values, all metabolite candidates were rapidly identified.As a consequence, 49 metabolites altogether, including archetype compound, were preliminarily characterised. The corresponding in vivo biotransformation processes, such as dehydration, dehydrogenation, hydroxylation, hydrogenation, methylation, sulphonation, N-acetylcysteine (NAC) formation, N-heterocyclisation and their composite reactions, were all discovered in the study.In conclusion, our results not only detailedly elucidated many new metabolites and metabolic pathways of swertiamarin, but also provided a reference for further study of its pharmacological mechanism and evaluation of its safety.
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Affiliation(s)
- Beibei Ma
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
| | - Tianyu Lou
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
| | - Tingting Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
| | - Ruiji Li
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
| | - Jinhui Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
| | - Shangyue Yu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
| | - Yudong Guo
- Beijing Institute for Drug Control, Beijing, China
| | - Zhibin Wang
- Beijing Tongrentang Research Institute, Beijing, China
| | - Jing Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, China
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