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Zhan H, Liu J, Fang Q, Huang Y, Chen X, Ni Y, Zhou L, Chen Z. Combining Fast Pure Shift NMR and GEMSTONE-Based Selective TOCSY for Efficient NMR Analysis of Complex Systems. Anal Chem 2024. [PMID: 39115999 DOI: 10.1021/acs.analchem.4c03146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
As one of the commonly used intact detection techniques, liquid NMR spectroscopy offers unparalleled insights into the chemical environments, structures, and dynamics of molecules. However, it generally encounters the challenges of crowded or even overlapped spectra, especially when probing complex sample systems containing numerous components and complicated molecular structures. Herein, we exploit a general NMR protocol for efficient NMR analysis of complex systems by combining fast pure shift NMR and GEMSTONE-based selective TOCSY. First, this protocol enables ultrahigh-selective observation on the coupling networks that are totally correlated with targeted resonances or components, even where they are situated in severely overlapped spectral regions. Second, pure shift simplification is introduced to enhance the spectral resolution and further resolve the subspectra containing spectral congestion, thus facilitating the dissection of overlapped spectra. Additionally, sparse sampling accompanied by spectral reconstruction is adopted to significantly accelerate acquisition and improve spectral quality. The advantages of this protocol were demonstrated on different complex sample systems, including a challenging compound of estradiol, a mixture of sucrose and d-glucose, and natural grape juice, verifying its feasibility and power, and boosting the potential application landscapes in various chemical fields.
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Affiliation(s)
- Haolin Zhan
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Jiawei Liu
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qiyuan Fang
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Xinyu Chen
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yang Ni
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lingling Zhou
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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Huang X, Chen L, Liu L, Chen H, Gong Z, Lyu J, Li Y, Jiang Q, Zeng X, Zhang P, Zhou H. Untargeted metabolomics analysis reveals the potential mechanism of imatinib-induced skin rash in patients with gastrointestinal stromal tumor. Int Immunopharmacol 2024; 140:112728. [PMID: 39098227 DOI: 10.1016/j.intimp.2024.112728] [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: 05/10/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 08/06/2024]
Abstract
Imatinib-induced skin rash poses a significant challenge for patients with gastrointestinal stromal tumor, often resulting in treatment interruption or discontinuation and subsequent treatment failure. However, the underlying mechanism of imatinib-induced skin rashes in gastrointestinal stromal tumor patients remains unclear. A total of 51 patients (27 with rash and 24 without rash) were enrolled in our study. Blood samples were collected concomitantly with the onset of clinical manifestations of rashes, and simultaneously collecting clinical relevant information. The imatinib concentration and untargeted metabolomics were performed by ultra-high-performance liquid chromatography-tandem mass spectrometry. There were no significant differences in age, gender, imatinib concentration and white blood cells count between the rash group and the control group. However, the rash group exhibited a higher eosinophil count (P<0.05) and lower lymphocyte count (P<0.05) compared to the control group. Untargeted metabolomics analysis found that 105 metabolites were significantly differentially abundant. The univariate analysis highlighted erucamide, linoleoylcarnitine, and valine betaine as potential predictive markers (AUC≥0.80). Further enriched pathway analysis revealed primary metabolic pathways, including sphingolipid signaling pathway, sphingolipid metabolism, cysteine and methionine metabolism, biosynthesis of unsaturated fatty acids, arginine and proline metabolism, and biosynthesis of amino acids. These findings suggest that the selected differential metabolites could serve as a foundation for the prediction and management of imatinib-induced skin rash in gastrointestinal stromal tumor patients.
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Affiliation(s)
- Xiao Huang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China
| | - Linhua Chen
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China
| | - Li Liu
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China
| | - Hefen Chen
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhujun Gong
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Department of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Lyu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yao Li
- Department of Gastrointestinal Surgery, Department of Nursing, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qi Jiang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiangyu Zeng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Peng Zhang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Hong Zhou
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China.
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Dhingra S, Zhang Z, Lohans CT, Brewitz L, Schofield CJ. Substitution of 2-oxoglutarate alters reaction outcomes of the Pseudomonas savastanoi ethylene-forming enzyme. J Biol Chem 2024; 300:107546. [PMID: 38992435 DOI: 10.1016/j.jbc.2024.107546] [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: 04/27/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
In seeding plants, biosynthesis of the phytohormone ethylene, which regulates processes including fruit ripening and senescence, is catalyzed by 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase. The plant pathogen Pseudomonas savastanoi (previously classified as: Pseudomonas syringae) employs a different type of ethylene-forming enzyme (psEFE), though from the same structural superfamily as ACC oxidase, to catalyze ethylene formation from 2-oxoglutarate (2OG) in an arginine dependent manner. psEFE also catalyzes the more typical oxidation of arginine to give L-Δ1-pyrroline-5-carboxylate (P5C), a reaction coupled to oxidative decarboxylation of 2OG giving succinate and CO2. We report on the effects of C3 and/or C4 substituted 2OG derivatives on the reaction modes of psEFE. 1H NMR assays, including using the pure shift method, reveal that, within our limits of detection, none of the tested 2OG derivatives is converted to an alkene; some are converted to the corresponding β-hydroxypropionate or succinate derivatives, with only the latter being coupled to arginine oxidation. The NMR results reveal that the nature of 2OG derivatization can affect the outcome of the bifurcating reaction, with some 2OG derivatives exclusively favoring the arginine oxidation pathway. Given that some of the tested 2OG derivatives are natural products, the results are of potential biological relevance. There are also opportunities for therapeutic or biocatalytic regulation of the outcomes of reactions catalyzed by 2OG-dependent oxygenases by the use of 2OG derivatives.
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Affiliation(s)
- Siddhant Dhingra
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Zhihong Zhang
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom.
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Milton LA, Davern JW, Hipwood L, Chaves JDS, McGovern J, Broszczak D, Hutmacher DW, Meinert C, Toh YC. Liver click dECM hydrogels for engineering hepatic microenvironments. Acta Biomater 2024:S1742-7061(24)00351-9. [PMID: 38960110 DOI: 10.1016/j.actbio.2024.06.037] [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: 01/22/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Decellularized extracellular matrix (dECM) hydrogels provide tissue-specific microenvironments which accommodate physiological cellular phenotypes in 3D in vitro cell cultures. However, their formation hinges on collagen fibrillogenesis, a complex process which limits regulation of physicochemical properties. Hence, achieving reproducible results with dECM hydrogels poses as a challenge. Here, we demonstrate that thiolation of solubilized liver dECM enables rapid formation of covalently crosslinked hydrogels via Michael-type addition, allowing for precise control over mechanical properties and superior organotypic biological activity. Investigation of various decellularization methodologies revealed that treatment of liver tissue with Triton X-100 and ammonium hydroxide resulted in near complete DNA removal with significant retention of the native liver proteome. Chemical functionalization of pepsin-solubilized liver dECMs via 1-ethyl-3(3-dimethylamino)propyl carbodiimide (EDC)/N-hydroxysuccinimide (NHS) coupling of l-Cysteine created thiolated liver dECM (dECM-SH), which rapidly reacted with 4-arm polyethylene glycol (PEG)-maleimide to form optically clear hydrogels under controlled conditions. Importantly, Young's moduli could be precisely tuned between 1 - 7 kPa by varying polymer concentrations, enabling close replication of healthy and fibrotic liver conditions in in vitro cell cultures. Click dECM-SH hydrogels were cytocompatible, supported growth of HepG2 and HepaRG liver cells, and promoted liver-specific functional phenotypes as evidenced by increased metabolic activity, as well CYP1A2 and CYP3A4 activity and excretory function when compared to monolayer culture and collagen-based hydrogels. Our findings demonstrate that click-functionalized dECM hydrogels offer a highly controlled, reproducible alternative to conventional tissue-derived hydrogels for in vitro cell culture applications. STATEMENT OF SIGNIFICANCE: Traditional dECM hydrogels face challenges in reproducibility and mechanical property control due to variable crosslinking processes. We introduce a click hydrogel based on porcine liver decellularized extracellular matrix (dECM) that circumnavigates these challenges. After optimizing liver decellularization for ECM retention, we integrated thiol-functionalized liver dECM with polyethylene-glycol derivatives through Michael-type addition click chemistry, enabling rapid, room-temperature gelation. This offers enhanced control over the hydrogel's mechanical and biochemical properties. The resultant click dECM hydrogels mimic the liver's natural ECM and exhibit greater mechanical tunability and handling ease, facilitating their application in high-throughput and industrial settings. Moreover, these hydrogels significantly improve the function of HepaRG-derived hepatocytes in 3D culture, presenting an advancement for liver tissue cell culture models for drug testing applications.
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Affiliation(s)
- Laura A Milton
- Faculty of Engineering, School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Australia; Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; Gelomics Pty Ltd, Brisbane, Australia
| | - Jordan W Davern
- Faculty of Engineering, School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Australia; Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; Gelomics Pty Ltd, Brisbane, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology, Brisbane, Australia
| | - Luke Hipwood
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; Gelomics Pty Ltd, Brisbane, Australia; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Juliana D S Chaves
- Cell & Molecular Biology Department, Mental Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jacqui McGovern
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology, Brisbane, Australia; Max Planck Queensland Centre (MPQC) for the Materials Science of Extracellular Matrices, Queensland University of Technology, Brisbane, Australia
| | - Daniel Broszczak
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Dietmar W Hutmacher
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology, Brisbane, Australia; Max Planck Queensland Centre (MPQC) for the Materials Science of Extracellular Matrices, Queensland University of Technology, Brisbane, Australia; Australian Research Council (ARC) Training Centre for Multiscale 3D Imaging, Modelling and Manufacturing (M3D Innovation), Queensland University of Technology, Brisbane, Australia
| | - Christoph Meinert
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; Gelomics Pty Ltd, Brisbane, Australia.
| | - Yi-Chin Toh
- Faculty of Engineering, School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Australia; Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology, Brisbane, Australia; Max Planck Queensland Centre (MPQC) for the Materials Science of Extracellular Matrices, Queensland University of Technology, Brisbane, Australia; Centre for Microbiome Research, Queensland University of Technology, Brisbane, Australia.
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Liu J, Liu S, Hui P, Teng S, Xie J, Sun Y. Ferrous ascorbate as a potential biomarker for diabetic retinopathy: a vitreous humour metabolomics study. BMC Ophthalmol 2024; 24:270. [PMID: 38914965 PMCID: PMC11194985 DOI: 10.1186/s12886-024-03530-6] [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: 03/15/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND This study aimed to explore differences in vitreous humour metabolites and metabolic pathways between patients with and without diabetic retinopathy (DR) and identify potential metabolite biomarkers. METHODS Clinical data and vitreous fluid samples were collected from 125 patients (40 without diabetes, 85 with DR). The metabolite profiles of the vitreous fluid samples were analysed using ultra-high performance liquid chromatography, Q-Exactive mass spectrometry, and multivariate statistical analysis. A machine learning model based on Least Absolute Shrinkage and Selection Operator Regularized logistic regression was used to build a risk scoring model based on selected metabolite levels. Candidate metabolites were regressed to glycated haemoglobin levels by a logistic regression model. RESULTS Twenty differential metabolites were identified between the DR and control groups and were significantly enriched in five Kyoto Encyclopedia of Genes and Genomes pathways (arginine biosynthesis; tricarboxylic acid cycle; alanine, aspartate, and glutamate metabolism; tyrosine metabolism; and D-glutamate metabolism). Ferrous ascorbate significantly contributes to poorer glycaemic control outcomes, offering insights into potential new pathogenic pathways in DR. CONCLUSIONS Disorders in the metabolic pathways of arginine biosynthesis, tricarboxylic acid cycle, alanine, aspartate, glutamate metabolism, tyrosine metabolism, and D-glutamate metabolism were associated with DR. Risk scores based on vitreous fluid metabolites can be used for the diagnosis and management of DR. Ferrous ascorbate can provide insights into potential new pathogenic pathways for DR.
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Affiliation(s)
- Jinmeng Liu
- Ophthalmology Department, First Hospital of Jilin University, No. 1 Xinmin Street, Changchun, 130021, Jilin province, China
| | - Shuang Liu
- Ophthalmology Department, First Hospital of Jilin University, No. 1 Xinmin Street, Changchun, 130021, Jilin province, China
| | - Peng Hui
- Ophthalmology Department, First Hospital of Jilin University, No. 1 Xinmin Street, Changchun, 130021, Jilin province, China
| | - Siying Teng
- Ophthalmology Department, First Hospital of Jilin University, No. 1 Xinmin Street, Changchun, 130021, Jilin province, China
| | - Jinghui Xie
- Ophthalmology Department, First Hospital of Jilin University, No. 1 Xinmin Street, Changchun, 130021, Jilin province, China
| | - Yabin Sun
- Ophthalmology Department, First Hospital of Jilin University, No. 1 Xinmin Street, Changchun, 130021, Jilin province, China.
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Bowen MB, Melendez B, Zhang Q, Moreno D, Peralta L, Chan WK, Jeter C, Tan L, Zal MA, Lorenzi PL, Dunner K, Yang RK, Broaddus RR, Celestino J, Gokul N, Whitley E, Schmandt R, Lu K, Kim HE, Yates MS. Mitochondrial defects and metabolic vulnerabilities in Lynch syndrome-associated MSH2-deficient endometrial cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.596841. [PMID: 38915709 PMCID: PMC11195112 DOI: 10.1101/2024.06.10.596841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Lynch syndrome (LS) is defined by inherited mutations in DNA mismatch repair genes, including MSH2, and carries 60% lifetime risk of developing endometrial cancer (EC). Beyond hypermutability, specific mechanisms for LS-associated endometrial carcinogenesis are not well understood. Here, we assessed the effects of MSH2 loss on EC pathogenesis using a novel mouse model (PR-Cre Msh2 flox/flox , abbreviated Msh2KO), primary cell lines established from this model, human tissues, and human EC cell lines with isogenic MSH2 knockdown. Beginning at eight months of age, 30% of Msh2KO mice exhibited endometrial atypical hyperplasia (AH), a precancerous lesion. At 12 to 16 months of age, 47% of Msh2KO mice exhibited either AH or ECs with histologic features similar to human LS-related ECs. Transcriptomic profiling of EC from Msh2KO mice revealed a transcriptomic signature for mitochondrial dysfunction. Studies in vitro and in vivo revealed mitochondrial dysfunction based upon two mechanisms: marked mitochondrial content reduction, along with pronounced disruptions to the integrity of retained mitochondria. Human LS-related ECs also exhibited mitochondrial content reduction compared with non-LS-related ECs. Functional studies revealed metabolic reprogramming of MSH2-deficient EC cells in vitro , including reduced oxidative phosphorylation and increased susceptibility to glycolysis suppression. We are the first to identify mitochondrial dysfunction and metabolic disruption as a consequence of MSH2 deficiency-related EC. Mitochondrial and metabolic aberrations should be evaluated as novel biomarkers for endometrial carcinogenesis or risk stratification and could serve as targets for cancer interception in women with LS. Significance This is the first study to report mitochondrial dysfunction contributing to MSH2-deficient endometrial cancer development, identifying a noncanonical pathway for MSH2 deficient carcinogenesis, which also imparts vulnerability to metabolic targeting.
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Mortoni A, Castelli E, Recca T, Quadrelli P. Structure of prolylrapamycin: confirmation through a revised and detailed NMR assignment study. J Antibiot (Tokyo) 2024; 77:345-352. [PMID: 38504121 PMCID: PMC11128375 DOI: 10.1038/s41429-024-00714-6] [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: 02/24/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
A complete and detailed characterization of Rapamycin (1) and Prolylrapamycin (2) has been conducted by homo- and hetero-nuclear NMR experiments in DMSO-d6 along with HRMS and FT-IR spectra and DSCs analyses. The NMR experiments allowed the assignment of every single proton and carbon atom belonging to the two structures and the definitive confirm of the presence of a pyrrolidine ring in Prolylrapamycin (2) in place of the piperidine ring that characterizes the structure of Sirolimus.
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Affiliation(s)
| | | | - Teresa Recca
- Centro Grandi Strumenti (CGS), Università degli Studi di Pavia, Via Bassi 21, 27100, Pavia, Italy
| | - Paolo Quadrelli
- Dipartimento di Chimica, Università degli Studi di Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
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Ketavarapu V, Addipilli R, Ragi N, Pallerla P, Simhadri V, Manne S, Sannapaneni K, Aslam M, Talukadar R, Ch VD, GV R, Amanchy R, Reddy DN, Sripadi P, Sasikala M. Plasma Metabolite Profiling Identifies Nondiabetic Chronic Pancreatitis Patients With Metabolic Alterations Progressing to Prediabetes Before HbA1c. Clin Transl Gastroenterol 2024; 15:e1. [PMID: 38661171 PMCID: PMC11196079 DOI: 10.14309/ctg.0000000000000704] [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: 01/30/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
INTRODUCTION Diabetes (T3cDM) secondary to chronic pancreatitis (CP) arises due to endocrine dysfunction and metabolic dysregulations. Currently, diagnostic tests are not available to identify patients who may progress from normoglycemia to hyperglycemia in CP. We conducted plasma metabolomic profiling to diagnose glycemic alterations early in the course of disease. METHODS Liquid chromatography-tandem mass spectrometry was used to generate untargeted, targeted plasma metabolomic profiles in patients with CP, controls (n = 445) following TRIPOD guidelines. Patients were stratified based on glucose tolerance tests following ADA guidelines. Multivariate analysis was performed using partial least squares discriminant analysis to assess discriminatory ability of metabolites among stratified groups. COMBIROC and logistic regression were used to derive biomarker signatures. AI-ML tool (Rapidminer) was used to verify these preliminary results. RESULTS Ceramide, lysophosphatidylethanolamine, phosphatidylcholine, lysophosphatidic acid (LPA), phosphatidylethanolamine, carnitine, and lysophosphatidylcholine discriminated T3cDM CP patients from healthy controls with AUC 93% (95% CI 0.81-0.98, P < 0.0001), and integration with pancreatic morphology improved AUC to 100% (95% CI 0.93-1.00, P < 0.0001). LPA, phosphatidylinositol, and ceramide discriminated nondiabetic CP with glycemic alterations (pre-diabetic CP); AUC 66% (95% CI 0.55-0.76, P = 0.1), and integration enhanced AUC to 74% (95% CI 0.55-0.88, P = 0.86). T3cDM was distinguished from prediabetic by LPA, phosphatidylinositol, and sphinganine (AUC 70%; 95% CI 0.54-0.83, P = 0.08), and integration improved AUC to 83% (95% CI 0.68-0.93, P = 0.05). CombiROC cutoff identified 75% and 78% prediabetes in validation 1 and 2 cohorts. Random forest algorithm assessed performance of integrated panel demonstrating AUC of 72% in predicting glycemic alterations. DISCUSSION We report for the first time that a panel of metabolites integrated with pancreatic morphology detects glycemia progression before HbA1c in patients with CP.
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Affiliation(s)
- Vijayasarathy Ketavarapu
- Translational Research Center, Asian Healthcare Foundation, AIG Hospitals, Mindspace Road, Gachibowli, Hyderabad, Telangana, India
| | - Ramunaidu Addipilli
- Centre for Mass Spectrometry, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana, India
| | - Nagarjunachary Ragi
- Centre for Mass Spectrometry, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana, India
| | - Pavankumar Pallerla
- Centre for Mass Spectrometry, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana, India
| | - Venu Simhadri
- Translational Research Center, Asian Healthcare Foundation, AIG Hospitals, Mindspace Road, Gachibowli, Hyderabad, Telangana, India
| | - Suvidha Manne
- Translational Research Center, Asian Healthcare Foundation, AIG Hospitals, Mindspace Road, Gachibowli, Hyderabad, Telangana, India
| | - Krishnaiah Sannapaneni
- Translational Research Center, Asian Healthcare Foundation, AIG Hospitals, Mindspace Road, Gachibowli, Hyderabad, Telangana, India
| | - Mohsin Aslam
- Asian Institute of Gastroenterology, Somajiguda, Hyderabad, Telangana, India
| | | | - Venkataramana Devi Ch
- Department of Biochemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Rao GV
- AIG Hospitals, Mindspace Road, Gachibowli, Hyderabad, Telangana, India
| | - Ramars Amanchy
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana, India
| | | | - Prabhakar Sripadi
- Centre for Mass Spectrometry, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana, India
| | - Mitnala Sasikala
- Translational Research Center, Asian Healthcare Foundation, AIG Hospitals, Mindspace Road, Gachibowli, Hyderabad, Telangana, India
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Jain SK, Bansal S, Bansal S, Singh B, Klotzbier W, Mehta KY, Cheema AK. An Optimized Method for LC-MS-Based Quantification of Endogenous Organic Acids: Metabolic Perturbations in Pancreatic Cancer. Int J Mol Sci 2024; 25:5901. [PMID: 38892088 PMCID: PMC11172734 DOI: 10.3390/ijms25115901] [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: 04/06/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Accurate and reliable quantification of organic acids with carboxylic acid functional groups in complex biological samples remains a major analytical challenge in clinical chemistry. Issues such as spontaneous decarboxylation during ionization, poor chromatographic resolution, and retention on a reverse-phase column hinder sensitivity, specificity, and reproducibility in multiple-reaction monitoring (MRM)-based LC-MS assays. We report a targeted metabolomics method using phenylenediamine derivatization for quantifying carboxylic acid-containing metabolites (CCMs). This method achieves accurate and sensitive quantification in various biological matrices, with recovery rates from 90% to 105% and CVs ≤ 10%. It shows linearity from 0.1 ng/mL to 10 µg/mL with linear regression coefficients of 0.99 and LODs as low as 0.01 ng/mL. The library included a wide variety of structurally variant CCMs such as amino acids/conjugates, short- to medium-chain organic acids, di/tri-carboxylic acids/conjugates, fatty acids, and some ring-containing CCMs. Comparing CCM profiles of pancreatic cancer cells to normal pancreatic cells identified potential biomarkers and their correlation with key metabolic pathways. This method enables sensitive, specific, and high-throughput quantification of CCMs from small samples, supporting a wide range of applications in basic, clinical, and translational research.
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Affiliation(s)
- Shreyans K. Jain
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
| | - Shivani Bansal
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
| | - Sunil Bansal
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
| | - Baldev Singh
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
| | - William Klotzbier
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
| | - Khyati Y. Mehta
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
| | - Amrita K. Cheema
- Department of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University Medical Center, E-415, New Research Building, 3900 Reservoir Road NW, Washington, DC 20057, USA; (S.K.J.); (S.B.); (S.B.); (B.S.); (W.K.); (K.Y.M.)
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Centre, Washington, DC 20057, USA
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10
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Jing G, Zuo J, Liu Z, Liu H, Cheng M, Yuan M, Gong H, Wu X, Song X. Mendelian randomization analysis reveals causal associations of serum metabolites with sepsis and 28-day mortality. Sci Rep 2024; 14:11551. [PMID: 38773119 PMCID: PMC11109149 DOI: 10.1038/s41598-024-58160-1] [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: 01/07/2024] [Accepted: 03/26/2024] [Indexed: 05/23/2024] Open
Abstract
Metabolic disorder has been found to be an important factor in the pathogenesis and progression of sepsis. However, the causation of such an association between serum metabolites and sepsis has not been established. We conducted a two-sample Mendelian randomization (MR) study. A genome-wide association study of 486 human serum metabolites was used as the exposure, whereas sepsis and sepsis mortality within 28 days were set as the outcomes. In MR analysis, 6 serum metabolites were identified to be associated with an increased risk of sepsis, and 6 serum metabolites were found to be related to a reduced risk of sepsis. Furthermore, there were 9 metabolites positively associated with sepsis-related mortality, and 8 metabolites were negatively correlated with sepsis mortality. In addition, "glycolysis/gluconeogenesis" (p = 0.001), and "pyruvate metabolism" (p = 0.042) two metabolic pathways were associated with the incidence of sepsis. This MR study suggested that serum metabolites played significant roles in the pathogenesis of sepsis, which may provide helpful biomarkers for early disease diagnosis, therapeutic interventions, and prognostic assessments for sepsis.
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Affiliation(s)
- Guoqing Jing
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jing Zuo
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhi Liu
- Department of Pediatrics, Children's Digital Health and Data Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huifan Liu
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Miao Cheng
- Jingmen Central Hospital, Jingmen, Hubei, China
| | - Min Yuan
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Hailong Gong
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaojing Wu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Xuemin Song
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
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11
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Chang Y, Dai T, Song G, Wang S, Pei H, Shen G, Feng J. Metabolomic analysis reveals the biological characteristics of giant congenital melanocytic nevi. J Pharm Biomed Anal 2024; 242:116060. [PMID: 38382316 DOI: 10.1016/j.jpba.2024.116060] [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: 01/12/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Giant congenital melanocytic nevi (GCMN) is a congenital cutaneous developmental deformity tumor that usually occurs at birth or in the first few weeks after birth, but its pathogenesis is still unclear. In this study, nuclear magnetic resonance-based metabolomics strategy was employed to evaluate the metabolic variations in serum and urine of the GCMN patients in order to understand its underlying biochemical mechanism and provide a potential intervention idea. Twenty-nine metabolites were observed to change significantly in serum and urine metabolomes, which are mainly involved in a variety of metabolic pathways including glyoxylate and dicarboxylate metabolism, TCA cycle and metabolisms of amino acids. The substantial cores of all the disturbed metabolic pathways are related to amino acid metabolism and carbohydrate metabolism and regulate the physiological state of the GCMN patients. Our results provide the physiological basis and physiological responses of GCMN and will be helpful for better understanding the molecular mechanisms of GCMN in future research.
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Affiliation(s)
- Yajie Chang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China
| | - Tao Dai
- Department of Wound Reconstructive Surgery, Tongji Hospital of Tongji University, Shanghai 200065, China.
| | - Ge Song
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China; Department of Plastic Surgery, First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471003, China
| | - Sanxi Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China
| | - Huile Pei
- Department of Dermatology, Second Affiliated Hospital Henan University of Science and Technology, Luoyang 471003, China
| | - Guiping Shen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China.
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China
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12
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Taoto C, Tangsrisakda N, Thukhammee W, Phetcharaburanin J, Iamsaard S, Tanphaichitr N. Rats Orally Administered with Ethyl Alcohol for a Prolonged Time Show Histopathology of the Epididymis and Seminal Vesicle Together with Changes in the Luminal Metabolite Composition. Biomedicines 2024; 12:1010. [PMID: 38790972 PMCID: PMC11117629 DOI: 10.3390/biomedicines12051010] [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: 02/06/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Prolonged ethanol (EtOH) consumption is associated with male infertility, with a decreased spermatogenesis rate as one cause. The defective maturation and development of sperm during their storage in the cauda epididymis and transit in the seminal vesicle can be another cause, possibly occurring before the drastic spermatogenesis disruption. Herein, we demonstrated that the cauda epididymis and seminal vesicle of rats, orally administered with EtOH under a regimen in which spermatogenesis was still ongoing, showed histological damage, including lesions, a decreased height of the epithelial cells and increased collagen fibers in the muscle layer, which implicated fibrosis. Lipid peroxidation (shown by malondialdehyde (MDA) levels) was observed, indicating that reactive oxygen species (ROS) were produced along with acetaldehyde during EtOH metabolism by CYP2E1. MDA, acetaldehyde and other lipid peroxidation products could further damage cellular components of the cauda epididymis and seminal vesicle, and this was supported by increased apoptosis (shown by a TUNEL assay and caspase 9/caspase 3 expression) in these two tissues of EtOH-treated rats. Consequently, the functionality of the cauda epididymis and seminal vesicle in EtOH-treated rats was impaired, as demonstrated by a decreases in 1H NMR-analyzed metabolites (e.g., carnitine, fructose), which were important for sperm development, metabolism and survival in their lumen.
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Affiliation(s)
- Chayakorn Taoto
- Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (C.T.); (N.T.)
| | - Nareelak Tangsrisakda
- Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (C.T.); (N.T.)
| | - Wipawee Thukhammee
- Research Institute for Human High Performance and Health Promotion, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Khon Kaen University Phenome Centre, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sitthichai Iamsaard
- Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (C.T.); (N.T.)
- Research Institute for Human High Performance and Health Promotion, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Nongnuj Tanphaichitr
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1Y 8L6, Canada
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13
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Shabnaz S, Nguyen TN, Williams R, Rubinstein SM, Garrett TJ, Tantawy M, Fradley MG, Alomar ME, Shain KH, Baz RC, Lenihan D, Cornell RF, Lu Q, Gong Y. Metabolomic signatures of carfilzomib-related cardiotoxicity in patients with multiple myeloma. Clin Transl Sci 2024; 17:e13828. [PMID: 38783568 PMCID: PMC11116757 DOI: 10.1111/cts.13828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/12/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
As a treatment for relapsed or refractory multiple myeloma (MM), carfilzomib has been associated with a significant risk of cardiovascular adverse events (CVAE). The goals of our study were to evaluate the metabolomic profile of MM patients to identify those at high risk prior to carfilzomib treatment and to explore the mechanisms of carfilzomib-CVAE to inform potential strategies to protect patients from this cardiotoxicity. Global metabolomic profiling was performed on the baseline and post-baseline plasma samples of 60 MM patients treated with carfilzomib-based therapy, including 31 who experienced CVAE, in a prospective cohort study. Baseline metabolites and post-baseline/baseline metabolite ratios that differ between the CVAE and no-CVAE patients were identified using unadjusted and adjusted methods. A baseline metabolomic risk score was created to stratify patients. We observed a lower abundance of tauroursodeoxycholic acid (T-UDCA) in CVAE patients at baseline (odds ratio [OR] = 0.47, 95% confidence interval [CI] = 0.21-0.94, p = 0.044) compared with the no-CVAE patients. A metabolite risk score was able to stratify patients into three risk groups. The area under the receiver-operating curve of the model with clinical predictors and metabolite risk score was 0.93. Glycochenodeoxycholic acid (OR = 0.56, 95% CI = 0.31-0.87, p = 0.023) was significantly lower in post-baseline/baseline ratios of CVAE patients compared with no-CVAE patients. Following metabolomic analysis, we created a baseline metabolite risk score that can stratify MM patients into different risk groups. The result also provided intriguing clues about the mechanism of carfilzomib-CVAE and potential cardioprotective strategies.
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Affiliation(s)
- Samia Shabnaz
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Trang N Nguyen
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Roy Williams
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Samuel M Rubinstein
- Department of Medicine, Division of Hematology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marwa Tantawy
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Michael G Fradley
- Cardio-Oncology Center of Excellence, Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mohammed E Alomar
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Kenneth H Shain
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Rachid C Baz
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Daniel Lenihan
- Cape Cardiology Group, Saint Francis Medical Center, Cape Girardeau, Missouri, USA
| | - Robert F Cornell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Qing Lu
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
- Cardio-Oncology Working Group, UF Health Cancer Center, Gainesville, Florida, USA
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14
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Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA. Paternal microbiome perturbations impact offspring fitness. Nature 2024; 629:652-659. [PMID: 38693261 PMCID: PMC11096121 DOI: 10.1038/s41586-024-07336-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
The gut microbiota operates at the interface of host-environment interactions to influence human homoeostasis and metabolic networks1-4. Environmental factors that unbalance gut microbial ecosystems can therefore shape physiological and disease-associated responses across somatic tissues5-9. However, the systemic impact of the gut microbiome on the germline-and consequently on the F1 offspring it gives rise to-is unexplored10. Here we show that the gut microbiota act as a key interface between paternal preconception environment and intergenerational health in mice. Perturbations to the gut microbiota of prospective fathers increase the probability of their offspring presenting with low birth weight, severe growth restriction and premature mortality. Transmission of disease risk occurs via the germline and is provoked by pervasive gut microbiome perturbations, including non-absorbable antibiotics or osmotic laxatives, but is rescued by restoring the paternal microbiota before conception. This effect is linked with a dynamic response to induced dysbiosis in the male reproductive system, including impaired leptin signalling, altered testicular metabolite profiles and remapped small RNA payloads in sperm. As a result, dysbiotic fathers trigger an elevated risk of in utero placental insufficiency, revealing a placental origin of mammalian intergenerational effects. Our study defines a regulatory 'gut-germline axis' in males, which is sensitive to environmental exposures and programmes offspring fitness through impacting placenta function.
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Affiliation(s)
- Ayele Argaw-Denboba
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Monica Di Giacomo
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Bobby Ranjan
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Saravanan Devendran
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Eleonora Mastrorilli
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Catrin T Lloyd
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Danilo Pugliese
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Violetta Paribeni
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Juliette Dabin
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Alessandra Pisaniello
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Sergio Espinola
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Alvaro Crevenna
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Subhanita Ghosh
- MRC London Institute for Medical Science (LMS), London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Neil Humphreys
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Olga Boruc
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Peter Sarkies
- MRC London Institute for Medical Science (LMS), London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Michael Zimmermann
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
- Department of Bioinformatics, Biozentrum, University of Würzburg, Würzburg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
| | - Jamie A Hackett
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy.
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15
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Pineda-Alegría JA, Peña-Rodríguez LM, Cardoso-Taketa A, Sánchez JE, Torres-Acosta JFDJ, Hernández-Bolio GI, Ortiz-Caltempa A, Villarreal ML, Aguilar-Marcelino L. 1H-NMR Metabolomic Study of the Mushroom Pleurotus djamor for the Identification of Nematocidal Compounds. Pharmaceuticals (Basel) 2024; 17:580. [PMID: 38794150 PMCID: PMC11124069 DOI: 10.3390/ph17050580] [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: 04/02/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Due to the increasing populations of anthelmintic-resistant gastrointestinal nematodes and as a consequence of the adverse effects of synthetic drugs, this study focuses on the search for secondary metabolites with nematocidal activity from the edible mushroom Pleurotus djamor using The proton nuclear magnetic resonance (1H-NMR) metabolomics. The highest activity was shown by the ethyl acetate fractions of mycelium (EC50 290.8 µg/mL) and basidiomes (EC50 282.7 µg/mL). Principal component analysis (PCA) and hierarchical data analysis (HCA) of the 1H-NMR metabolic profiles data showed that the ethanolic extracts, the ethyl acetate, butanol, and water fractions from mycelium have different metabolic profiles than those from basidiomes, while low polarity (hexane) fractions from both stages of fungal development show similar profiles. Orthogonal partial least squares discriminant analysis (OPLS-DA) allowed the identification of signals in the 1H-NMR metabolic profile associated with nematocidal activity. The signals yielded via OPLS-DA and bidimensional NMR analysis allowed the identification of uracil as a component in the ethyl acetate fraction from basidiomes, with an EC50 of 237.7 µg/mL. The results obtained showed that chemometric analyses of the 1H-NMR metabolic profiles represent a viable strategy for the identification of bioactive compounds from samples with complex chemical profiles.
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Affiliation(s)
- Jesús Antonio Pineda-Alegría
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (J.A.P.-A.); (A.C.-T.); (A.O.-C.)
| | | | - Alexandre Cardoso-Taketa
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (J.A.P.-A.); (A.C.-T.); (A.O.-C.)
| | - José E. Sánchez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km. 2.5, Tapachula 30700, Chiapas, Mexico;
| | - Juan Felipe de Jesús Torres-Acosta
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Km 15.5 Carretera Mérida-Xmatkuil, Mérida 97100, Yucatán, Mexico;
| | - Gloria Ivonne Hernández-Bolio
- Departamento de Física Aplicada, Centro de Investigación y Estudios Avanzados (CINVESTAV), Unidad Mérida, Mérida 97205, Yucatán, Mexico;
| | - Anabel Ortiz-Caltempa
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (J.A.P.-A.); (A.C.-T.); (A.O.-C.)
| | - María Luisa Villarreal
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (J.A.P.-A.); (A.C.-T.); (A.O.-C.)
| | - Liliana Aguilar-Marcelino
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Km 11 Carretera Federal Cuernavaca-Cuautla, No. 8534, Jiutepec 62550, Morelos, Mexico
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16
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Janthamala S, Promraksa B, Thanee M, Duenngai K, Jusakul A, Kongpetch S, Kraiklang R, Thanee K, Pinlaor P, Namwat N, Saya H, Techasen A. Anticancer properties and metabolomic profiling of Shorea roxburghii extracts toward gastrointestinal cancer cell lines. BMC Complement Med Ther 2024; 24:178. [PMID: 38689275 PMCID: PMC11061966 DOI: 10.1186/s12906-024-04479-1] [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: 11/25/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Gastrointestinal cancer (GIC) ranks as the highest cause of cancer-related deaths globally. GIC patients are often diagnosed at advanced stages, limiting effective treatment options. Chemotherapy, the common GIC recommendation, has significant disadvantages such as toxicity and adverse effects. Natural products contain substances with diverse pharmacological characteristics that promise for use in cancer therapeutics. In this study, the flower of renowned Asian medicinal plant, Shorea roxburghii was collected and extracted to investigate its phytochemical contents, antioxidant, and anticancer properties on GIC cells. METHODS The phytochemical contents of Shorea roxburghii extract were assessed using suitable methods. Phenolic content was determined through the Folin-Ciocalteu method, while flavonoids were quantified using the aluminum chloride (AlCl3) method. Antioxidant activity was evaluated using the FRAP and DPPH assays. Cytotoxicity was assessed in GIC cell lines via the MTT assay. Additionally, intracellular ROS levels and apoptosis were examined through flow cytometry techniques. The correlation between GIC cell viability and phytochemicals, 1H-NMR analysis was conducted. RESULTS Among the four different solvent extracts, ethyl acetate extract had the highest phenolic and flavonoid contents. Water extract exhibited the strongest reducing power and DPPH scavenging activity following by ethyl acetate. Interestingly, ethyl acetate extract demonstrated the highest inhibitory activity against three GIC cell lines (KKU-213B, HepG2, AGS) with IC50 values of 91.60 µg/ml, 39.38 µg/ml, and 35.59 µg/ml, while showing less toxicity to normal fibroblast cells. Ethyl acetate extract induced reactive oxygen species and apoptosis in GIC cell lines by downregulating anti-apoptotic protein Bcl-2. Metabolic profiling-based screening revealed a positive association between reduced GIC cell viability and phytochemicals like cinnamic acid and its derivatives, ferulic acid and coumaric acid. CONCLUSIONS This study highlights the potential of natural compounds in Shorea roxburghii in the development of more effective and safer anticancer agents as options for GIC as well as shedding light on new avenues for cancer treatment.
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Affiliation(s)
- Sutthiwan Janthamala
- Biomedical Sciences Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand
| | - Bundit Promraksa
- Regional Medical Sciences Center 2 Phitsanulok, Department of Medical Sciences, Ministry of Public Health, Phitsanulok, Thailand
| | - Malinee Thanee
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kunyarat Duenngai
- Department of Thai Traditional Medicine, Faculty of Science and Technology, Phetchabun Rajabhat University, Phetchabun, Thailand
| | - Apinya Jusakul
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Sarinya Kongpetch
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ratthaphol Kraiklang
- Nutrition for Health Program, Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand
| | - Kidsada Thanee
- Faculty of Public Health, Ubon Ratchathani Rajabhat University, Ubon Ratchathani, Thailand
| | - Porntip Pinlaor
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Nisana Namwat
- Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Hideyuki Saya
- Cancer Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Anchalee Techasen
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
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17
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Wen S, Lin X, Luo W, Pan Y, Liao F, Wang Z, Zhan B, Feng J, Huang H. Metabolic difference between patient-derived xenograft model of pancreatic ductal adenocarcinoma and corresponding primary tumor. BMC Cancer 2024; 24:485. [PMID: 38632504 PMCID: PMC11022326 DOI: 10.1186/s12885-024-12193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Patients-derived xenograft (PDX) model have been widely used for tumor biological and pathological studies. However, the metabolic similarity of PDX tumor to the primary cancer (PC) is still unknown. METHODS In present study, we established PDX model by engrafting primary tumor of pancreatic ductal adenocarcinoma (PDAC), and then compared the tumor metabolomics of PC, the first generation of PDX tumor (PDXG1), and the third generation of PDX tumor (PDXG3) by using 1H NMR spectroscopy. Then, we assessed the differences in response to chemotherapy between PDXG1 and PDXG3 and corresponding metabolomic differences in drug-resistant tumor tissues. To evaluate the metabolomic similarity of PDX to PC, we also compared the metabolomic difference of cell-derived xenograft (CDX) vs. PC and PDX vs. PC. RESULTS After engraftment, PDXG1 tumor had a low level of lactate, pyruvate, citrate and multiple amino acids (AAs) compared with PC. Metabolite sets enrichment and metabolic pathway analyses implied that glycolysis metabolisms were suppressed in PDXG1 tumor, and tricarboxylic acid cycle (TCA)-associated anaplerosis pathways, such as amino acids metabolisms, were enhanced. Then, after multiple passages of PDX, the altered glycolysis and TCA-associated anaplerosis pathways were partially recovered. Although no significant difference was observed in the response of PDXG1 and PDXG3 to chemotherapy, the difference in glycolysis and amino acids metabolism between PDXG1 and PDXG3 could still be maintained. In addition, the metabolomic difference between PC and CDX models were much larger than that of PDX model and PC, indicating that PDX model still retain more metabolic characteristics of primary tumor which is more suitable for tumor-associated metabolism research. CONCLUSIONS Compared with primary tumor, PDX models have obvious difference in metabolomic level. These findings can help us design in vivo tumor metabolomics research legitimately and analyze the underlying mechanism of tumor metabolic biology thoughtfully.
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Affiliation(s)
- Shi Wen
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Xianchao Lin
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Wei Luo
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Yu Pan
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Fei Liao
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Zhenzhao Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China
| | - Bohan Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China.
| | - Heguang Huang
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China.
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18
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Novoa J, López-Ibáñez J, Chagoyen M, Ranea JAG, Pazos F. CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. Database (Oxford) 2024; 2024:baae025. [PMID: 38564426 PMCID: PMC10986793 DOI: 10.1093/database/baae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/01/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
The CoMentG resource contains millions of relationships between terms of biomedical interest obtained from the scientific literature. At the core of the system is a methodology for detecting significant co-mentions of concepts in the entire PubMed corpus. That method was applied to nine sets of terms covering the most important classes of biomedical concepts: diseases, symptoms/clinical signs, molecular functions, biological processes, cellular compartments, anatomic parts, cell types, bacteria and chemical compounds. We obtained more than 7 million relationships between more than 74 000 terms, and many types of relationships were not available in any other resource. As the terms were obtained from widely used resources and ontologies, the relationships are given using the standard identifiers provided by them and hence can be linked to other data. A web interface allows users to browse these associations, searching for relationships for a set of terms of interests provided as input, such as between a disease and their associated symptoms, underlying molecular processes or affected tissues. The results are presented in an interactive interface where the user can explore the reported relationships in different ways and follow links to other resources. Database URL: https://csbg.cnb.csic.es/CoMentG/.
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Affiliation(s)
- Jorge Novoa
- Computational Systems Biology, National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3., Madrid 28049 , Spain
| | - Javier López-Ibáñez
- Computational Systems Biology, National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3., Madrid 28049 , Spain
| | - Mónica Chagoyen
- Computational Systems Biology, National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3., Madrid 28049 , Spain
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, Avda. Cervantes, 2., Málaga 29071, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Biomedical Research in Malaga and platform of nanomedicine (IBIMA platform BIONAND), Malaga 29071, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona 08034, Spain
| | - Florencio Pazos
- Computational Systems Biology, National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3., Madrid 28049 , Spain
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19
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Peruzzotti-Jametti L, Willis CM, Krzak G, Hamel R, Pirvan L, Ionescu RB, Reisz JA, Prag HA, Garcia-Segura ME, Wu V, Xiang Y, Barlas B, Casey AM, van den Bosch AMR, Nicaise AM, Roth L, Bates GR, Huang H, Prasad P, Vincent AE, Frezza C, Viscomi C, Balmus G, Takats Z, Marioni JC, D'Alessandro A, Murphy MP, Mohorianu I, Pluchino S. Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature 2024; 628:195-203. [PMID: 38480879 PMCID: PMC10990929 DOI: 10.1038/s41586-024-07167-9] [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: 10/03/2022] [Accepted: 02/06/2024] [Indexed: 03/17/2024]
Abstract
Sustained smouldering, or low-grade activation, of myeloid cells is a common hallmark of several chronic neurological diseases, including multiple sclerosis1. Distinct metabolic and mitochondrial features guide the activation and the diverse functional states of myeloid cells2. However, how these metabolic features act to perpetuate inflammation of the central nervous system is unclear. Here, using a multiomics approach, we identify a molecular signature that sustains the activation of microglia through mitochondrial complex I activity driving reverse electron transport and the production of reactive oxygen species. Mechanistically, blocking complex I in pro-inflammatory microglia protects the central nervous system against neurotoxic damage and improves functional outcomes in an animal disease model in vivo. Complex I activity in microglia is a potential therapeutic target to foster neuroprotection in chronic inflammatory disorders of the central nervous system3.
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Affiliation(s)
- L Peruzzotti-Jametti
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - C M Willis
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - G Krzak
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - R Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - L Pirvan
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - R-B Ionescu
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - J A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - H A Prag
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - M E Garcia-Segura
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - V Wu
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Y Xiang
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - B Barlas
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - A M Casey
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - A M R van den Bosch
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - A M Nicaise
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - L Roth
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - G R Bates
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - H Huang
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - P Prasad
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - A E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - C Frezza
- University Hospital Cologne, Cologne, Germany
| | | | - G Balmus
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania
| | - Z Takats
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - J C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - A D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - M P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - S Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK.
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20
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Lievens E, Van Vossel K, Van de Casteele F, Derave W, Murdoch JB. The effects of residual dipolar coupling on carnosine in proton muscle spectra. NMR IN BIOMEDICINE 2024; 37:e5083. [PMID: 38217329 DOI: 10.1002/nbm.5083] [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: 05/25/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 01/15/2024]
Abstract
Carnosine, an MR-visible dipeptide in human muscle, is well characterized by two peaks at ~8 and ~7 ppm from C2 and C4 imidazole protons. Like creatine and other metabolites, carnosine is subject to residual dipolar coupling in the anisotropic environment of muscle fibers, but the effects have not been studied extensively. Single-voxel TE 30-32 PRESS spectra from three different 3T studies were acquired from gastrocnemius medialis and soleus muscles in the human lower leg. In these studies, carnosine T2 values were measured, and spectra were obtained at three different foot angles. LCModel was used to fit the carnosine peaks with a basis set that was generated using shaped RF pulses and included a range of dipolar couplings affecting the C4 peak. A seven-parameter analytic expression was used to fit the CH2 doublets of creatine. It incorporated an optimized "effective TE" value to model the effect of shaped RF pulses. The fits confirm that the triplet C4 peak of carnosine is dipolar coupled to a pair of CH2 protons, with no need to include a contribution from a separate pool of freely rotating uncoupled carnosine. Moreover, the couplings experienced by carnosine C4 protons and creatine CH2 protons are strongly correlated (R2 = 0.88, P<0.001), exhibiting a similar 3cos2 θ - 1 dependence on the angle θ between fiber orientation and B0. T2 values for the singlet C2 peak of gastrocnemius carnosine are inversely proportional to the C4 dipolar coupling strength (R2 = 0.97, P < 0.001), which in turn is a function of foot orientation. This dependence indicates that careful positioning of the foot while acquiring lower leg muscle spectra is important to obtain reproducible carnosine concentrations. As proton magnetic resonance spectroscopy of carnosine is currently used to non-invasively estimate the muscle fiber typology, these results have important implications in sport science.
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Affiliation(s)
- Eline Lievens
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Kim Van Vossel
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | | | - Wim Derave
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - James B Murdoch
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
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21
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Ethier R, Krishnamurthy A, Jeffrey M, Tompkins TA. Profiling of Metabolites in a Fermented Soy Dietary Supplement Reinforces its Role in the Management of Intestinal Inflammation. Mol Nutr Food Res 2024; 68:e2300770. [PMID: 38522032 DOI: 10.1002/mnfr.202300770] [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: 10/31/2023] [Revised: 02/19/2024] [Indexed: 03/25/2024]
Abstract
SCOPE Gastro-AD (GAD) is a soy flour derived product that undergoes an industrial fermentation with Lactobacillus delbrueckii R0187 and has demonstrated clinical effects in gastroesophageal reflux and peptic ulcer symptom resolution. The aim of this study is to describe and link GAD's metabolomic profile to plausible mechanisms that manifest and explain the documented clinical outcomes. METHODS AND RESULTS 1H NMR spectroscopy with multivariate statistical analysis is used to characterize the prefermented soy flour and GAD products. The acquired spectra are screened using various resources and the molecular assignments are confirmed using total correlation spectroscopy (TOCSY). Peaks corresponding to different metabolites are integrated and compared between the two products for relative changes. HPLC and GC are used to quantify some specific molecules. NMR analyses demonstrate significant changes in the composition of various assigned bioactive moieties. HPLC and GC analysis demonstrate deglycation of isoflavones after fermentation, resulting in estrogenically active secondary metabolites that have been previously shown to help to reduce inflammation. CONCLUSION The identification of bioactive molecules, such as genistein and SCFAs, capable of modulating anti-inflammatory signaling cascades in the stomach's gastric and neuroendocrine tissues can explain the reported biological effects in GAD and is supported by in vivo data.
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Affiliation(s)
- Richard Ethier
- Richard Ethier Consulting, Montreal, Quebec, H4C 2J9, Canada
| | - Arun Krishnamurthy
- Purity-IQ Inc., Suite# 102, 150 Research Lane, Guelph, Ontario, N1G 4T2, Canada
| | - Michael Jeffrey
- Faculty of Science, Engineering & Information Technology, Durham College, Oshawa, Ontario, L1G 0C5, Canada
| | - Thomas A Tompkins
- Lallemand Bio-Ingredients, 1620 rue Prefontaine, Montreal, Quebec, H1W 2N8, Canada
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22
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Singh R, Fatima E, Thakur L, Singh S, Ratan C, Kumar N. Advancements in CHO metabolomics: techniques, current state and evolving methodologies. Front Bioeng Biotechnol 2024; 12:1347138. [PMID: 38600943 PMCID: PMC11004234 DOI: 10.3389/fbioe.2024.1347138] [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: 11/30/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background: Investigating the metabolic behaviour of different cellular phenotypes, i.e., good/bad grower and/or producer, in production culture is important to identify the key metabolite(s)/pathway(s) that regulate cell growth and/or recombinant protein production to improve the overall yield. Currently, LC-MS, GC-MS and NMR are the most used and advanced technologies for investigating the metabolome. Although contributed significantly in the domain, each technique has its own biasness towards specific metabolites or class of metabolites due to various reasons including variability in the concept of working, sample preparation, metabolite-extraction methods, metabolite identification tools, and databases. As a result, the application of appropriate analytical technique(s) is very critical. Purpose and scope: This review provides a state-of-the-art technological insights and overview of metabolic mechanisms involved in regulation of cell growth and/or recombinant protein production for improving yield from CHO cultures. Summary and conclusion: In this review, the advancements in CHO metabolomics over the last 10 years are traced based on a bibliometric analysis of previous publications and discussed. With the technical advancement in the domain of LC-MS, GC-MS and NMR, metabolites of glycolytic and nucleotide biosynthesis pathway (glucose, fructose, pyruvate and phenylalanine, threonine, tryptophan, arginine, valine, asparagine, and serine, etc.) were observed to be upregulated in exponential-phase thereby potentially associated with cell growth regulation, whereas metabolites/intermediates of TCA, oxidative phosphorylation (aspartate, glutamate, succinate, malate, fumarate and citrate), intracellular NAD+/NADH ratio, and glutathione metabolic pathways were observed to be upregulated in stationary-phase and hence potentially associated with increased cell-specific productivity in CHO bioprocess. Moreover, each of technique has its own bias towards metabolite identification, indicating their complementarity, along with a number of critical gaps in the CHO metabolomics pipeline and hence first time discussed here to identify their potential remedies. This knowledge may help in future study designs to improve the metabolomic coverage facilitating identification of the metabolites/pathways which might get missed otherwise and explore the full potential of metabolomics for improving the CHO bioprocess performances.
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Affiliation(s)
- Rita Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Eram Fatima
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sevaram Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Chandra Ratan
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Niraj Kumar
- Translational Health Science and Technology Institute, Faridabad, India
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23
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Zhou J, Chen JQ, Gong S, Ban YJ, Zhang L, Liu Y, Wu JL, Li N. Isolation, Bioactivity, and Molecular Docking of a Rare Gastrodin Isocitrate and Diverse Parishin Derivatives from Gastrodia elata Blume. ACS OMEGA 2024; 9:14520-14529. [PMID: 38559968 PMCID: PMC10976414 DOI: 10.1021/acsomega.4c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Gastrodia elata Blume (G. elata) is a well-known medicine food homology plant widely used in treating neurological disorders such as Alzheimer's disease (AD). Here, undiscovered gastrodin derivatives were systematically studied. Seven novel gastrodin derivatives (1-7), including a unique gastrodin isocitrate (1) and six differently substituted parishin derivatives (2-7), were isolated. Structural identification was mainly based on 1D and 2D NMR data, high-resolution ESI-MS data, and HPLC analysis. Notably, the stereochemistry of 1 was further elucidated by ECD calculations. Compounds 1 and 6 showed neuroprotective effects on the H2O2-induced PC12 cell injury model. Molecular docking analysis exhibited that 1 and 6 had good affinities with three popular AD-related targets. These findings not only enriched the chemical diversity but also revealed potential active components in G. elata.
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Affiliation(s)
- Jie Zhou
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
| | - Jia-Qian Chen
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
| | - Shilin Gong
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
| | - Yu-Juan Ban
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
| | - Li Zhang
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
| | - Ying Liu
- School
of Basic Medicinal Sciences and Nursing, Chengdu University, Chengdu 610106, PR China
| | - Jian-Lin Wu
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
| | - Na Li
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa 999078 SAR, China
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24
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Thaiwatcharamas K, Loilome W, Ho PN, Chusilp S, Tanming P, Klanrit P, Phetcharaburanin J. Children with Hirschsprung disease exhibited alterations in host-microbial co-metabolism after pull-through operation. Pediatr Surg Int 2024; 40:87. [PMID: 38512700 DOI: 10.1007/s00383-024-05667-3] [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] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
PURPOSE This study aims to compare the fecal metabolome in post pull-through HD with and without HAEC patients and healthy young children using nuclear magnetic resonance (NMR) spectroscopy. METHODS Fresh fecal samples were collected from children under 5 years of age in both post-pull-through HD patients and healthy Thai children. A total of 20 fecal samples were then analyzed using NMR spectroscopy. RESULTS Thirty-four metabolites identified among HD and healthy children younger than 5 years were compared. HD samples demonstrated a significant decrease in acetoin, phenylacetylglutamine, and N-acetylornithine (corrected p value = 0.01, 0.04, and 0.004, respectively). Succinate and xylose significantly decreased in HD with HAEC group compared to HD without HAEC group (corrected p value = 0.04 and 0.02, respectively). Moreover, glutamine and glutamate metabolism, and alanine, aspartate, and glutamate metabolism were the significant pathways involved, with pathway impact 0.42 and 0.50, respectively (corrected p value = 0.02 and 0.04, respectively). CONCLUSION Differences in class, quantity, and metabolism of protein and other metabolites in young children with HD after pull-through operation were identified. Most of the associated metabolic pathways were correlated with the amino acids metabolism, which is required to maintain intestinal integrity and function.
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Affiliation(s)
| | - Watcharin Loilome
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Phuc N Ho
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sinobol Chusilp
- Department of Surgery, Division of Pediatric Surgery, Khon Kaen University, Khon Kaen, Thailand
| | - Patchareeporn Tanming
- Department of Surgery, Division of Pediatric Surgery, Khon Kaen University, Khon Kaen, Thailand
| | - Poramate Klanrit
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
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25
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Ma L, Chen C, Zhao C, Li T, Ma L, Jiang J, Duan Z, Si Q, Chuang TH, Xiang R, Luo Y. Targeting carnitine palmitoyl transferase 1A (CPT1A) induces ferroptosis and synergizes with immunotherapy in lung cancer. Signal Transduct Target Ther 2024; 9:64. [PMID: 38453925 PMCID: PMC10920667 DOI: 10.1038/s41392-024-01772-w] [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: 09/02/2023] [Revised: 12/26/2023] [Accepted: 02/08/2024] [Indexed: 03/09/2024] Open
Abstract
Despite the successful application of immune checkpoint therapy, no response or recurrence is typical in lung cancer. Cancer stem cells (CSCs) have been identified as a crucial player in immunotherapy-related resistance. Ferroptosis, a form of cell death driven by iron-dependent lipid peroxidation, is highly regulated by cellular metabolism remolding and has been shown to have synergistic effects when combined with immunotherapy. Metabolic adaption of CSCs drives tumor resistance, yet the mechanisms of their ferroptosis defense in tumor immune evasion remain elusive. Here, through metabolomics, transcriptomics, a lung epithelial-specific Cpt1a-knockout mouse model, and clinical analysis, we demonstrate that CPT1A, a key rate-limiting enzyme of fatty acid oxidation, acts with L-carnitine, derived from tumor-associated macrophages to drive ferroptosis-resistance and CD8+ T cells inactivation in lung cancer. Mechanistically, CPT1A restrains ubiquitination and degradation of c-Myc, while c-Myc transcriptionally activates CPT1A expression. The CPT1A/c-Myc positive feedback loop further enhances the cellular antioxidant capacity by activating the NRF2/GPX4 system and reduces the amount of phospholipid polyunsaturated fatty acids through ACSL4 downregulating, thereby suppressing ferroptosis in CSCs. Significantly, targeting CPT1A enhances immune checkpoint blockade-induced anti-tumor immunity and tumoral ferroptosis in tumor-bearing mice. The results illustrate the potential of a mechanism-guided therapeutic strategy by targeting a metabolic vulnerability in the ferroptosis of CSCs to improve the efficacy of lung cancer immunotherapy.
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Affiliation(s)
- Lei Ma
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Chong Chen
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Chunxing Zhao
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tong Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Lingyu Ma
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Jiayu Jiang
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhaojun Duan
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Qin Si
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Rong Xiang
- Department of Immunology, Nankai University, Tianjin, 300071, China
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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26
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van Tetering L, Spies S, Wildeman QDK, Houthuijs KJ, van Outersterp RE, Martens J, Wevers RA, Wishart DS, Berden G, Oomens J. A spectroscopic test suggests that fragment ion structure annotations in MS/MS libraries are frequently incorrect. Commun Chem 2024; 7:30. [PMID: 38355930 PMCID: PMC10867025 DOI: 10.1038/s42004-024-01112-7] [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: 11/18/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Modern untargeted mass spectrometry (MS) analyses quickly detect and resolve thousands of molecular compounds. Although features are readily annotated with a molecular formula in high-resolution small-molecule MS applications, the large majority of them remains unidentified in terms of their full molecular structure. Collision-induced dissociation tandem mass spectrometry (CID-MS2) provides a diagnostic molecular fingerprint to resolve the molecular structure through a library search. However, for de novo identifications, one must often rely on in silico generated MS2 spectra as reference. The ability of different in silico algorithms to correctly predict MS2 spectra and thus to retrieve correct molecular structures is a topic of lively debate, for instance in the CASMI contest. Underlying the predicted MS2 spectra are the in silico generated product ion structures, which are normally not used in de novo identification, but which can serve to critically assess the fragmentation algorithms. Here we evaluate in silico generated MSn product ion structures by comparison with structures established experimentally by infrared ion spectroscopy (IRIS). For a set of three dozen product ion structures from five precursor molecules, we find that virtually all fragment ion structure annotations in three major in silico MS2 libraries (HMDB, METLIN, mzCloud) are incorrect and caution the reader against their use for structure annotation of MS/MS ions.
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Affiliation(s)
- Lara van Tetering
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Sylvia Spies
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Quirine D K Wildeman
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Kas J Houthuijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands
| | - David S Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands.
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.
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27
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Krikunova PV, Tolordava ER, Arkharova NA, Karimov DN, Bukreeva TV, Shirinian VZ, Khaydukov EV, Pallaeva TN. Riboflavin Crystals with Extremely High Water Solubility. ACS APPLIED MATERIALS & INTERFACES 2024; 16:5504-5512. [PMID: 38278768 DOI: 10.1021/acsami.3c15853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
New insights into the unique biochemical properties of riboflavin (Rf), also known as vitamin B2, are leading to the development of its use not only as a vitamin supplement but also as a potential anti-inflammatory, immunomodulatory, antioxidant, anticancer, and antiviral agent, where it may play a role as an inhibitor of viral proteinases. At the same time, the comparison of the pharmacoactivity of Rf with its known metabolites, namely, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), is very complicated due to its poor water solubility: 0.1-0.3 g/L versus 67 g/L for FMN and 50 g/L for FAD, which is the limiting factor for its administration in clinical practice. In this study, we report the recrystallization procedure of the type A Rf crystals into the slightly hydrophobic type B/C and a new hydrophilic crystal form that has been termed the P type. Our method of Rf crystal modification based on recrystallization from dilute alkaline solution provides an unprecedented extremely high water solubility of Rf, reaching 23.5 g/L. A comprehensive study of the physicochemical properties of type P riboflavin showed increased photodynamic therapeutic activity compared to the known types A and B/C against clinical isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Salmonella typhimurium. Importantly, our work not only demonstrates a simple and inexpensive method for the synthesis of riboflavin with high solubility, which should lead to increased bioactivity, but also opens up opportunities for improving both known and new therapeutic applications of vitamin B2.
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Affiliation(s)
| | - Eteri R Tolordava
- Gamaleya Research Institute of Epidemiology and Microbiology, Moscow 123098, Russia
| | | | - Denis N Karimov
- FSRC "Crystallography and Photonics" RAS, Moscow 119333, Russia
| | | | - Valerii Z Shirinian
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
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28
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Domżał B, Nawrocka EK, Gołowicz D, Ciach MA, Miasojedow B, Kazimierczuk K, Gambin A. Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts. Anal Chem 2024; 96:188-196. [PMID: 38117933 PMCID: PMC10782418 DOI: 10.1021/acs.analchem.3c03594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
1H NMR spectroscopy is a powerful tool for analyzing mixtures including determining the concentrations of individual components. When signals from multiple compounds overlap, this task requires computational solutions. They are typically based on peak-picking and the comparison of obtained peak lists with libraries of individual components. This can fail if peaks are not sufficiently resolved or when peak positions differ between the library and the mixture. In this paper, we present Magnetstein, a quantification algorithm rooted in the optimal transport theory that makes it robust to unexpected frequency shifts and overlapping signals. Thanks to this, Magnetstein can quantitatively analyze difficult spectra with the estimation trueness an order of magnitude higher than that of commercial tools. Furthermore, the method is easier to use than other approaches, having only two parameters with default values applicable to a broad range of experiments and requiring little to no preprocessing of the spectra.
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Affiliation(s)
- Barbara Domżał
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Ewa Klaudia Nawrocka
- Centre
of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Dariusz Gołowicz
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Michał Aleksander Ciach
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Błażej Miasojedow
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | | | - Anna Gambin
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
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29
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Peruzzotti-Jametti L, Willis CM, Hamel R, Krzak G, Reisz JA, Prag HA, Wu V, Xiang Y, van den Bosch AMR, Nicaise AM, Roth L, Bates GR, Huang H, Vincent AE, Frezza C, Viscomi C, Marioni JC, D'Alessandro A, Takats Z, Murphy MP, Pluchino S. Mitochondrial reverse electron transport in myeloid cells perpetuates neuroinflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574059. [PMID: 38260262 PMCID: PMC10802366 DOI: 10.1101/2024.01.03.574059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Sustained smouldering, or low grade, activation of myeloid cells is a common hallmark of several chronic neurological diseases, including multiple sclerosis (MS) 1 . Distinct metabolic and mitochondrial features guide the activation and the diverse functional states of myeloid cells 2 . However, how these metabolic features act to perpetuate neuroinflammation is currently unknown. Using a multiomics approach, we identified a new molecular signature that perpetuates the activation of myeloid cells through mitochondrial complex II (CII) and I (CI) activity driving reverse electron transport (RET) and the production of reactive oxygen species (ROS). Blocking RET in pro-inflammatory myeloid cells protected the central nervous system (CNS) against neurotoxic damage and improved functional outcomes in animal disease models in vivo . Our data show that RET in myeloid cells is a potential new therapeutic target to foster neuroprotection in smouldering inflammatory CNS disorders 3 .
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30
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Nemadodzi LE, Managa GM. 1H NMR-Based Metabolomics Profile of Green and Red Amaranthus Grown in Open Field versus Greenhouse Cultivation System. Metabolites 2023; 14:21. [PMID: 38248824 PMCID: PMC10819972 DOI: 10.3390/metabo14010021] [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: 11/25/2023] [Revised: 12/24/2023] [Accepted: 12/26/2023] [Indexed: 01/23/2024] Open
Abstract
Traditionally, indigenous African leafy vegetables such as Amaranthus, blackjack, jute mallow, cleome monophyla, and spider plants have been conventionally and organically grown as weeds in open fields. However, the lack of land space due to the increase in population has resulted in unconventional, modern, and advanced agricultural farming. The introduction of a greenhouse has recently become the second most popular growing system alongside shade net and glasshouse to increase productivity and meet consumers' demand. Several studies on Amaranthus species have solely focused on physiological parameters and nutritional composition, leaving a huge gap on their metabolomic profile of the leaves which is crucial to comprehend when growing Amaranthus species in different cropping systems. Therefore, the study aimed to determine the influence of different cropping systems on the release of metabolites of two commonly consumed Amaranthus species in South Africa. H1 -Nuclear Magnetic Resonance (NMR) tool was used to profile the untargeted metabolites of green (Amaranthus graecizans L.) and red (Amaranthus cruentus L.) species. A total of 12 metabolites-trehalose, betaine, glutamine, choline, sucrose, caprate, adenosine, asparagine, carnitine, caffeine, aspartate, and alanine-were detected in green amaranth grown in open fields. Except for caffeine, aspartate, and caprate, which were found in the green amaranth grown in open fields, all the other metabolites were detected in the greenhouse grown once. Interestingly, allantoin, which serves as an allelochemical, was the sole distinct metabolite detected in greenhouse cultivated green amaranth. On the contrary, seven similar metabolites were quantified in red amaranth grown in both open fields and greenhouses, apart from caffeine, which was only detected in greenhouse-cultivated red amaranth.
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Affiliation(s)
- Lufuno Ethel Nemadodzi
- Department of Agriculture and Animal Health, University of South Africa, Johannesburg 1709, South Africa
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31
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Gawin-Mikołajewicz A, Nawrot U, Malec KH, Krajewska K, Nartowski KP, Karolewicz BL. The Effect of High-Pressure Homogenization Conditions on the Physicochemical Properties and Stability of Designed Fluconazole-Loaded Ocular Nanoemulsions. Pharmaceutics 2023; 16:11. [PMID: 38276489 PMCID: PMC10818809 DOI: 10.3390/pharmaceutics16010011] [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: 09/13/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024] Open
Abstract
The growing interest in high-energy emulsification is a result of its scalability, which is important from an industrial perspective and allows for a more reproducible and efficient production of pharmaceutical formulations. The aim of this study was to evaluate the effect of composition, mainly a fixed surfactant/cosurfactant (Smix) ratio, their concentration, and the parameters of high-pressure homogenization (HPH) processing on the quality and stability of ophthalmic fluconazole-loaded nanoemulsions. After a physicochemical analysis of nanoemulsions containing 20% w/w of oil, as optimal conditions for the HPH process, three cycles at a pressure of 1000 bar were established, obtaining formulations with an average droplet diameter size in the range of 80.63-129.68 nm and PDI values below 0.25. While it was expected that an increasing cosurfactant concentration decreased the droplet size, in the case of formulations containing Tween 20 and 10% w/w of cosurfactants, "over-processing" was observed, identified by the droplet size and polydispersity index increase. Consecutively, the selected formulations were evaluated for in vitro drug release in Franz's cell, antifungal activity, and 30-day stability using NMR spectroscopy. An antifungal activity test showed no significant difference in the antifungal activity between optimal fluconazole-loaded nanoemulsions and a 0.3% aqueous drug solution, but previously, research showed that prepared formulations were characterized by a higher viscosity and satisfactory prolonged release compared to a control. In a 30-day stability study, it was observed that higher HLB values of the used surfactants decreased the stability of the formulations in the following order: Kolliphor EL, Tween 80, Tween 20. The NMR spectra confirmed that Kolliphor EL-based formulations ensured the higher stability of the nanoemulsion composition in comparison to Tween 80 and a better stabilizing effect of propylene glycol as a cosurfactant in comparison to PEG 200. Therefore, the optimization of HPH technology should be focused on the selection of Smix and the Smix:oil ratio in order to prepare stable formulations of high quality.
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Affiliation(s)
- Agnieszka Gawin-Mikołajewicz
- Department of Drug Form Technology, Wroclaw Medical University, 211A Borowska Str., 50-556 Wroclaw, Poland; (K.H.M.); (K.K.); (K.P.N.); (B.L.K.)
| | - Urszula Nawrot
- Department of Pharmaceutical Microbiology and Parasitology, Wroclaw Medical University, 211A Borowska Str., 50-556 Wroclaw, Poland;
| | - Katarzyna Hanna Malec
- Department of Drug Form Technology, Wroclaw Medical University, 211A Borowska Str., 50-556 Wroclaw, Poland; (K.H.M.); (K.K.); (K.P.N.); (B.L.K.)
| | - Karolina Krajewska
- Department of Drug Form Technology, Wroclaw Medical University, 211A Borowska Str., 50-556 Wroclaw, Poland; (K.H.M.); (K.K.); (K.P.N.); (B.L.K.)
| | - Karol Przemysław Nartowski
- Department of Drug Form Technology, Wroclaw Medical University, 211A Borowska Str., 50-556 Wroclaw, Poland; (K.H.M.); (K.K.); (K.P.N.); (B.L.K.)
| | - Bożena Lucyna Karolewicz
- Department of Drug Form Technology, Wroclaw Medical University, 211A Borowska Str., 50-556 Wroclaw, Poland; (K.H.M.); (K.K.); (K.P.N.); (B.L.K.)
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32
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Macias S, Yilmaz A, Kirma J, Moore SE, Woodside JV, Graham SF, Green BD. Non-targeted LC-MS/MS metabolomic profiling of human plasma uncovers a novel Mediterranean diet biomarker panel. Metabolomics 2023; 20:3. [PMID: 38066384 PMCID: PMC10709258 DOI: 10.1007/s11306-023-02058-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023]
Abstract
INTRODUCTION Consumption of a Mediterranean diet (MD) has established health benefits, and the identification of novel biomarkers could enable objective monitoring of dietary pattern adherence. OBJECTIVES The present investigation performed untargeted metabolomics on blood plasma from a controlled study of MD adherence, to identify novel blood-based metabolite biomarkers associated with the MD pattern, and to build a logistic regression model that could be used to characterise MD adherence. METHODS A hundred and thirty-five plasma samples from n = 58 patients collected at different time points were available. Using a 14-point scale MD Score (MDS) subjects were divided into 'high' or 'low' MDS adherence groups and liquid chromatography-mass spectrometry (LC-MS/MS) was applied for analysis. RESULTS The strongest association with MDS was pectenotoxin 2 seco acid (r = 0.53; ROC = 0.78), a non-toxic marine xenobiotic metabolite. Several lipids were useful biomarkers including eicosapentaenoic acid, the structurally related lysophospholipid (20:5(5Z,8Z,11Z,14Z,17Z)/0:0), a phosphatidylcholine (P-18:1(9Z)/16:0) and also xi-8-hydroxyhexadecanedioic acid. Two metabolites negatively correlated with MDS, these were the monoacylglycerides (0:0/16:1(9Z)/0:0) and (0:0/20:3(5Z,8Z,11Z)/0:0). By stepwise elimination we selected a panel of 3 highly discriminatory metabolites and developed a linear regression model which identified 'high MDS' individuals with high sensitivity and specificity [AUC (95% CI) 0.83 (0.76-0.97)]. CONCLUSION Our study highlights the utility of metabolomics as an approach for developing novel panels of dietary biomarkers. Quantitative profiling of these metabolites is required to validate their utility for evaluating dietary adherence.
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Affiliation(s)
- Shirin Macias
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Ali Yilmaz
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI, 48073, USA
| | - Joseph Kirma
- Michigan Medicine University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah E Moore
- Centre for Public Health, Queen's University Belfast, Belfast, BT12 6BA, UK
| | - Jayne V Woodside
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, BT12 6BA, UK
| | - Stewart F Graham
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI, 48073, USA
- Department of Obstetrics and Gynaecology, Corewell Health William Beaumont University Hospital, 3601 W.13 Mile Road, Royal Oak, MI, 48073, USA
| | - Brian D Green
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK.
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Priscila Busch Furlan C, Berilli Batista P, Akemi Kido L, Garbellini Duft R, Regina Cavaglieri C, de Oliveira Carvalho P, Roberto Maróstica Junior M. Synergistic effect rescue animal model from NASH caused by diet-inflammation inducer. Food Res Int 2023; 174:113562. [PMID: 37986439 DOI: 10.1016/j.foodres.2023.113562] [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: 03/21/2023] [Revised: 10/03/2023] [Accepted: 10/09/2023] [Indexed: 11/22/2023]
Abstract
Excessive intake of pro-inflammatory fatty acids is related to the development of insulin resistance, impaired oxidative stress enzymes, and lipid disorders, leading to inflammation and development of non-alcoholic steatohepatitis (NASH). Diet and physical exercise are considered to prevent and treat metabolic disorders caused by chronic inflammatory states (responsible for insulin resistance and diabetes type 2) in individuals with obesity and nonalcoholic fatty liver diseases (NAFLD). Our investigation tested the hypothesis that Hass avocado oil, a monounsaturated fatty acid and a source of phytosterol, may improve liver and metabolic parameters without adverse effects when combined with physical exercise. Rats ingested a high-fat diet for seven weeks and were then subjected to more six weeks with a standard diet, Hass avocado-oil ingestion, and swimming. The intervention showed significantly improvements by synergistic effect between Hass avocado-oil and swimming exercise (P < 0.05), including improving adiponectin, leptin, and fasting blood glucose levels, alleviating insulin resistance, reducing serum TNF-α, improving glutathione enzyme levels, and decreasing lipotoxicity in the liver and blood and serum triacylglycerides in blood (P < 0.05). Liver tissue markers of apoptosis and necrosis such as CK-18 filaments and dimethylamine (DMA) were significantly higher in the intervention group (P < 0.05). We were unable to fully confirm our hypothesis. Although the synergistic effects between Hass avocado-oil and the swimming regimen offer a promising chance of recovering liver health by improving 10 health biological markers, we must not ignore the cellular damage due to apoptosis and necrosis in liver cells and DMA. The data on metabolomic profile and avocado-oil-treated livers highlight the need for further investigation.
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Affiliation(s)
- Cibele Priscila Busch Furlan
- Department of Food and Nutrition, Faculty of Food Engineering, University of Campinas, UNICAMP, Campinas, SP, Brazil
| | - Patricia Berilli Batista
- Department of Food and Nutrition, Faculty of Food Engineering, University of Campinas, UNICAMP, Campinas, SP, Brazil
| | - Larissa Akemi Kido
- Department of Food and Nutrition, Faculty of Food Engineering, University of Campinas, UNICAMP, Campinas, SP, Brazil
| | - Renata Garbellini Duft
- Laboratory of Exercise Physiology, Faculty of Physical Education, University of Campinas, UNICAMP, Campinas, SP, Brazil
| | - Claudia Regina Cavaglieri
- Laboratory of Exercise Physiology, Faculty of Physical Education, University of Campinas, UNICAMP, Campinas, SP, Brazil
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Fuentes CA, Öztop MH, Rojas-Rioseco M, Bravo M, Göksu AÖ, Manley M, Castillo RDP. Application of segmented analysis via multivariate curve resolution with alternating least squares to 1H-nuclear magnetic resonance spectroscopy to identify different sugar sources. Food Chem 2023; 428:136817. [PMID: 37459678 DOI: 10.1016/j.foodchem.2023.136817] [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: 04/11/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 07/31/2023]
Abstract
The different types of sugar employed in the food industry exhibit chemical similarity and are mostly dominated by sucrose. Owing to the sugar origin of and differences in production, the presence of certain minor organic compounds differs. To differentiate between sugars based on their botanical source, geographical origin, or storage conditions, commercial brown sugars and sugar beet extracts were analyzed by 1H NMR spectroscopy applying a segmented analysis by means of multivariate curve resolution-alternating least squares (MCR-ALS). Principal component analysis and partial least squares-discriminant analysis yielded excellent differentiation between sugars from different sources after the application of this preprocessing strategy; without loss of chemical information and with direct interpretation of the results. By applying a segmented analysis via MCR-ALS to 1H NMR sugar data, similar spectroscopic profiles could be differentiated. This improved the selectivity of 1H NMR spectroscopy for sugar source differentiation which can be useful for industrial sugar authentication purposes.
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Affiliation(s)
- Cristian A Fuentes
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción 4070386, Chile; Laboratorio de Bioespectroscopia y Quimiometría (BioSpeQ), Centro de Biotecnología, Universidad de Concepción, Concepción 4070386, Chile
| | - Mecit Halil Öztop
- Department of Food Engineering, Middle East Technical University, Ankara 06800, Turkey
| | - Macarena Rojas-Rioseco
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción 4070386, Chile; Laboratorio de Bioespectroscopia y Quimiometría (BioSpeQ), Centro de Biotecnología, Universidad de Concepción, Concepción 4070386, Chile
| | - Martín Bravo
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción 4070386, Chile; Laboratorio de Bioespectroscopia y Quimiometría (BioSpeQ), Centro de Biotecnología, Universidad de Concepción, Concepción 4070386, Chile
| | - Aylin Özgür Göksu
- Kayseri Sugar R&D Center, Kayseri Sugar Factory, Kayseri 38070, Turkey
| | - Marena Manley
- Deparment of Food Science, Stellenbosch University, Private Bag X1, Matieland (Stellenbosch) 7602, South Africa.
| | - Rosario Del P Castillo
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción 4070386, Chile; Laboratorio de Bioespectroscopia y Quimiometría (BioSpeQ), Centro de Biotecnología, Universidad de Concepción, Concepción 4070386, Chile
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35
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Chang Y, Chen J, Huang R, Wu J, Lin Y, Li Q, Shen G, Feng J. Identification of potential biomarkers in malnutrition children with severity by 1H-NMR-based metabolomics: a preliminary study in the Chinese population. Eur J Nutr 2023; 62:3193-3205. [PMID: 37550595 DOI: 10.1007/s00394-023-03224-7] [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: 03/28/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
PURPOSE Child malnutrition is a global public health problem, but the underlying pathophysiologic mechanisms with severity remain poorly understood, and the potential biomarkers served to the clinical diagnosis are still not available. This study aimed to identify the serum metabolic characteristics of malnourished children with severity. METHODS Fasted overnight serum samples were collected following clinical standard procedures among 275 malnourished and 199 healthy children from the Women and Children's Hospital, Xiamen University Child Health Department from July 2020 to May 2022. Nuclear magnetic resonance (NMR)-based metabolomics strategy was applied to identify the potential serum biomarkers of malnutrition from 275 malnourished children aged 4 to 84 months with mild (Mil, 199 cases), moderate (Mod, 101 cases), and severe (Sev, 7 cases) malnutrition. RESULTS Ten, fifteen, and fifteen differential metabolites were identified from the Mil, Mod, and Sev malnutrition groups, respectively. Eight common metabolites, including increased acetoacetate, acetone, ethanol, succinate, 3-hydroxybutyrate, and decreased alanine, methionine, and N-acetyl-glycoprotein, could be the potential biomarkers for malnourished children. The altered metabolic pathways were mainly related to energy metabolism and amino acid metabolism via the network-based pathway enrichment. CONCLUSION Eight potential biomarkers, including acetoacetate, acetone, ethanol, succinate, 3-hydroxybutyrate, alanine, methionine, and N-acetyl-glycoprotein, could characterize the child malnutrition. Child malnutrition-induced abnormal energy metabolism, impaired nutrition utilization and the reduced nutrient availability, and more metabolic disturbance will appear with the severity. Our results are valuable for further studies on the etiology and pathogenesis of malnutrition for clinical intervention and improvement.
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Affiliation(s)
- Yajie Chang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Xiamen, 361005, Fujian, China
| | - Jing Chen
- Department of Child Health, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, Fujian, China
| | - Rong Huang
- Department of Child Health, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, Fujian, China
| | - Jinxia Wu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Xiamen, 361005, Fujian, China
| | - Yanyan Lin
- Department of Child Health, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, Fujian, China
| | - Quanquan Li
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Xiamen, 361005, Fujian, China
| | - Guiping Shen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Xiamen, 361005, Fujian, China.
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Xiamen, 361005, Fujian, China
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Tang C, Li X, Wang T, Wang J, Xiao M, He M, Chang X, Fan Y, Li Y. Characterization of Metabolite Landscape Distinguishes Medicinal Fungus Cordyceps sinensis and other Cordyceps by UHPLC-Q Exactive HF-X Untargeted Metabolomics. Molecules 2023; 28:7745. [PMID: 38067475 PMCID: PMC10708286 DOI: 10.3390/molecules28237745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Cordyceps represent a valuable class of medicinal fungi with potential utilization. The overexploitation and resource scarcity of Cordyceps sinensis (CS) have led to the emergence of Cordyceps such as Cordyceps militaris (CM) and Cordyceps cicadae (CC) as substitutes. The medicinal value of CS is often considered superior to other Cordyceps, potentially owing to differences in active ingredients. This study aimed to evaluate the differences in the composition and abundance of the primary and secondary metabolites of CS and its substitutes by untargeted metabolomics. A total of 4671 metabolites from 18 superclasses were detected. CS and its substitutes were rich in amino acids, lipids, organic acids, and their derivatives. We statistically analyzed the metabolites and found a total of 285 differential metabolites (3'-Adenylic acid, O-Adipoylcarnitine, L-Dopachrome, etc.) between CS and CC, CS and CM, and CM and CC, which are potential biomarkers. L-glutamate and glycerophospholipids were differential metabolites. A KEGG enrichment analysis indicated that the tyrosine metabolic pathway and tryptophan metabolism pathway are the most differentially expressed pathways among the three Cordyceps. In contrast, CS was enriched in a higher abundance of most lipid metabolites when compared to CM and CC, which may be an indispensable foundation for the pharmacological functions of CS. In conclusion, systematic, untargeted metabolomics analyses for CS and other Cordyceps have delivered a precious resource for insights into metabolite landscapes and predicted potential components of disease therapeutics.
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Affiliation(s)
- Chuyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
| | - Xiuzhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
| | - Tao Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
| | - Jie Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
| | - Mengjun Xiao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
| | - Min He
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
| | - Xiyun Chang
- Qinghai Institute of Health Sciences, Xining 810000, China;
| | - Yuejun Fan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
| | - Yuling Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China; (C.T.); (X.L.); (T.W.); (M.X.); (M.H.)
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Huang G, Zhou Y, Cheng H, Lv T, Zheng L, Li C, Chen Y. Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection. Front Microbiol 2023; 14:1273949. [PMID: 38029192 PMCID: PMC10644037 DOI: 10.3389/fmicb.2023.1273949] [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: 08/07/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Enterococcus faecium is a common pathogen responsible for urinary tract infections (UTIs) and often establishes extensive colonization within the intestinal tract. Our aim was to assess the genomic and transcriptomic differences between colonized E. faecium without UTI (only-colonization) and colonized E. faecium causing UTI (endogenous infections). Method We investigated the correlation between fecal isolates from the same patient and UTI-causing isolates using PFGE and WGS, and classified fecal isolates into two groups: those that solely colonized and those associated with endogenous urinary tract infections. We characterized the genomes of colonization-only and endogenously infected isolates by Scoary GWAS, and the transcriptomes of the isolates at 3 h urine exposure to assess pathogen-related changes. Result Based on PFGE and WGS, eight isolates of endogenously infected E. faecium and nine isolates of only-colonized E. faecium were characterized and carbon and nitrogen regulated metabolisms such as genes encoding the phosphotransferase (PTS) system were enriched in endogenously infected E. faecium. Transcriptome analysis revealed significant differences in gene expression in the PTS system, lysine synthesis, galactose metabolism and citrate import between endogenously infected and only-colonized E. faecium isolates, highlighting the important role of certain carbon regulatory genes in the colonization and survival of endogenously infected E. faecium. Conclusion In only-colonized and endogenously infected isolates, we observed differential expression patterns of genes related to carbon metabolism and amino acids, suggesting that metabolic diversity is a strategy for isolates leading to endogenous infection.
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Affiliation(s)
- Ge Huang
- Department of Clinical Laboratory Center, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
- Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Yizheng Zhou
- Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Hai Cheng
- Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Tao Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lisi Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chengbin Li
- Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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Kumar BS. Recent Advances and Applications of Ambient Mass Spectrometry Imaging in Cancer Research: An Overview. Mass Spectrom (Tokyo) 2023; 12:A0129. [PMID: 37789912 PMCID: PMC10542858 DOI: 10.5702/massspectrometry.a0129] [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: 07/18/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
Cancer metabolic variability has a significant impact on both diagnosis and treatment outcomes. The discovery of novel biological indicators and metabolic dysregulation, can significantly rely on comprehension of the modified metabolism in cancer, is a research focus. Tissue histology is a critical feature in the diagnostic testing of many ailments, such as cancer. To assess the surgical margin of the tumour on patients, frozen section histology is a tedious, laborious, and typically arbitrary method. Concurrent monitoring of ion images in tissues facilitated by the latest advancements in mass spectrometry imaging (MSI) is far more efficient than optical tissue image analysis utilized in conventional histopathology examination. This article focuses on the "desorption electrospray ionization (DESI)-MSI" technique's most recent advancements and uses in cancer research. DESI-MSI can provide wealthy information based on the variances in metabolites and lipids in normal and cancerous tissues by acquiring ion images of the lipid and metabolite variances on biopsy samples. As opposed to a systematic review, this article offers a synopsis of the most widely employed cutting-edge DESI-MSI techniques in cancer research.
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Affiliation(s)
- Bharath S. Kumar
- Correspondence to: Bharath S. Kumar, 21, B2, 27th Street, Nanganallur, Chennai, India, e-mail:
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Li T, Zhang K, Niu X, Chen W, Yang X, Gong X, Tu P, Wang Y, Liu W, Song Y. MS/MS fingerprint comparison between adjacent generations enables substructure identification: Flavonoid glycosides as cases. J Pharm Biomed Anal 2023; 234:115559. [PMID: 37393693 DOI: 10.1016/j.jpba.2023.115559] [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: 03/26/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
MS/MS spectrum matching currently serves as a favored means to identify the concerned metabolites attributing to the accessibility of several famous databases. However, the rule that takes the entire structure into account frequently leads to "0 hit" when inquiring MS/MS (usually MS2) spectrum in the databases. Conjugation plays an important role for the high-level structural diversity of metabolites in all organisms, and a given conjugate usually consists of two or more substructures. If MS3 spectra participate in database retrieval, the structural annotation potential of those databases should be dramatically expanded via identifying substructures. Attributing to the ubiquitous distribution pattern, flavonoid glycosides were deployed as the representative family to justify whether the primary fragment ion termed as Y0+, resulted from neutral loss of glycosyl residue(s), generated identical MS3 spectrum with MS2 spectrum of the aglycone cation namely [A+H]+. Because of owning unique ability to measure MS/MS spectrum with the exactly desired exciting energy, linear ion trap chamber of Qtrap-MS was responsible for generating the desired MS3 and MS2 spectra. When taking both m/z and ion intensity features into consideration, the findings included: 1) glycosides sharing identical aglycones produced the same MS3 spectra for Y0+; 2) different MS3 spectra for Y0+ occurred amongst glycosides bearing distinct, even isomeric, aglycones; 3) isomeric aglycones generated different MS2 spectra; and 4) MS3 spectra for Y0+ agreed with MS2 spectra of [A+H]+ when comparing paired glycoside and aglycone. Together, fingerprint comparison between MS3 and MS2 spectra could structurally annotate the substructures and further advance MS/MS spectrum matching towards the identification of, but not limited to, aglycones for flavonoid glycosides.
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Affiliation(s)
- Ting Li
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ke Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaoya Niu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wei Chen
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiangfen Yang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xingcheng Gong
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa 999078, Macao
| | - Wenjing Liu
- School of Pharmacy, Henan University of Chinese Medicine, Jinshui East Road, Zhengdong New District, Zhengzhou 450046, China.
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
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Branzoli F, Liserre R, Deelchand DK, Poliani PL, Bielle F, Nichelli L, Sanson M, Lehéricy S, Marjańska M. Neurochemical Differences between 1p/19q Codeleted and Noncodeleted IDH-mutant Gliomas by in Vivo MR Spectroscopy. Radiology 2023; 308:e223255. [PMID: 37668523 PMCID: PMC10546286 DOI: 10.1148/radiol.223255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 09/06/2023]
Abstract
Background Noninvasive identification of glioma subtypes is important for optimizing treatment strategies. Purpose To compare the in vivo neurochemical profiles between isocitrate dehydrogenase (IDH) 1-mutant 1p/19q codeleted gliomas and their noncodeleted counterparts measured by MR spectroscopy at 3.0 T with a point-resolved spectroscopy (PRESS) sequence optimized for D-2-hydroxyglutarate (2HG) detection. Materials and Methods Adults with IDH1-mutant gliomas were retrospectively included for this study from two university hospitals (inclusion period: January 2015 to July 2016 and September 2019 to June 2021, respectively) based on availability of 1p/19q codeletion status and a PRESS acquisition optimized for 2HG detection (echo time, 97 msec) at 3.0 T before any treatment. Spectral analysis was performed using LCModel and a simulated basis set. Metabolite quantification was performed using the water signal as a reference and correcting for water and metabolite longitudinal and transverse relaxation time constants. Concentration ratios were computed using total creatine (tCr) and total choline. A two-tailed unpaired t test was used to compare metabolite concentrations obtained in codeleted versus noncodeleted gliomas, accounting for multiple comparisons. Results Thirty-one adults (mean age, 39 years ± 8 [SD]; 19 male) were included, and 19 metabolites were quantified. Cystathionine concentration was higher in codeleted (n = 13) than noncodeleted (n = 18) gliomas when quantification was performed using the water signal or tCr as references (2.33 mM ± 0.98 vs 0.93 mM ± 0.94, and 0.34 mM ± 0.14 vs 0.14 mM ± 0.14, respectively; both P < .001). The sensitivity and specificity of PRESS to detect codeletion by means of cystathionine quantification were 92% and 61%, respectively. Other metabolites did not show evidence of a difference between groups (P > .05). Conclusion Higher cystathionine levels were detected in IDH1-mutant 1p/19q codeleted gliomas than in their noncodeleted counterparts with use of a PRESS sequence optimized for 2HG detection. Of 19 metabolites quantified, only cystathionine showed evidence of a difference in concentration between groups. Clinical trial registry no. NCT01703962 © RSNA, 2023 See also the editorial by Lin in this issue.
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Affiliation(s)
- Francesca Branzoli
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Roberto Liserre
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Dinesh K. Deelchand
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Pietro Luigi Poliani
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Franck Bielle
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Lucia Nichelli
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Marc Sanson
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Stéphane Lehéricy
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
| | - Małgorzata Marjańska
- From the Sorbonne University, UMR S 1127, Inserm U 1127, CNRS UMR 7225, Paris Brain Institute–L’Institut du Cerveau et de la Moelle Épinière (ICM), 47 boulevard de l’Hôpital, 75013 Paris, France (F. Branzoli, L.N., M.S., S.L.); Center for Neuroimaging Research (CENIR), L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (F. Branzoli, S.L.); Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy (R.L.); Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minn (D.K.D., M.M.); Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy (P.L.P.); Laboratory R Escourolle (F. Bielle), Department of Neuroradiology (L.N., S.L.), and Department of Neurology 2 (M.S.), University Hospital La Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France; and Onconeurotek Tumor Bank, L’Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France (M.S.)
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Abdelkader Y, Perez-Davalos L, LeDuc R, Zahedi RP, Labouta HI. Omics approaches for the assessment of biological responses to nanoparticles. Adv Drug Deliv Rev 2023; 200:114992. [PMID: 37414362 DOI: 10.1016/j.addr.2023.114992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.
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Affiliation(s)
- Yasmin Abdelkader
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt
| | - Luis Perez-Davalos
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada
| | - Richard LeDuc
- Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada
| | - Hagar I Labouta
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521.
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Lemas DJ, Du X, Dado-Senn B, Xu K, Dobrowolski A, Magalhães M, Aristizabal-Henao JJ, Young BE, Francois M, Thompson LA, Parker LA, Neu J, Laporta J, Misra BB, Wane I, Samaan S, Garrett TJ. Untargeted Metabolomic Analysis of Lactation-Stage-Matched Human and Bovine Milk Samples at 2 Weeks Postnatal. Nutrients 2023; 15:3768. [PMID: 37686800 PMCID: PMC10490210 DOI: 10.3390/nu15173768] [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: 07/26/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Epidemiological data demonstrate that bovine whole milk is often substituted for human milk during the first 12 months of life and may be associated with adverse infant outcomes. The objective of this study is to interrogate the human and bovine milk metabolome at 2 weeks of life to identify unique metabolites that may impact infant health outcomes. Human milk (n = 10) was collected at 2 weeks postpartum from normal-weight mothers (pre-pregnant BMI < 25 kg/m2) that vaginally delivered term infants and were exclusively breastfeeding their infant for at least 2 months. Similarly, bovine milk (n = 10) was collected 2 weeks postpartum from normal-weight primiparous Holstein dairy cows. Untargeted data were acquired on all milk samples using high-resolution liquid chromatography-high-resolution tandem mass spectrometry (HR LC-MS/MS). MS data pre-processing from feature calling to metabolite annotation was performed using MS-DIAL and MS-FLO. Our results revealed that more than 80% of the milk metabolome is shared between human and bovine milk samples during early lactation. Unbiased analysis of identified metabolites revealed that nearly 80% of milk metabolites may contribute to microbial metabolism and microbe-host interactions. Collectively, these results highlight untargeted metabolomics as a potential strategy to identify unique and shared metabolites in bovine and human milk that may relate to and impact infant health outcomes.
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Affiliation(s)
- Dominick J. Lemas
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
- Department of Obstetrics and Gynecology, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
- Center for Perinatal Outcomes Research, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Bethany Dado-Senn
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Ke Xu
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Amanda Dobrowolski
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Marina Magalhães
- Department of Behavioral Nursing Science, College of Nursing, University of Florida, Gainesville, FL 32603, USA;
| | - Juan J. Aristizabal-Henao
- Department of Physiological Science, Center for Environmental and Human Toxicology, College of Veterinary Science, University of Florida, Gainesville, FL 32608, USA;
| | - Bridget E. Young
- Division of Breastfeeding and Lactation Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Magda Francois
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Lindsay A. Thompson
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Leslie A. Parker
- Center for Perinatal Outcomes Research, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Josef Neu
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Jimena Laporta
- Department of Obstetrics and Gynecology, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | | | - Ismael Wane
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Samih Samaan
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
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Eltemur D, Robatscher P, Oberhuber M, Scampicchio M, Ceccon A. Applications of Solution NMR Spectroscopy in Quality Assessment and Authentication of Bovine Milk. Foods 2023; 12:3240. [PMID: 37685173 PMCID: PMC10486658 DOI: 10.3390/foods12173240] [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: 07/06/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is emerging as a promising technique for the analysis of bovine milk, primarily due to its non-destructive nature, minimal sample preparation requirements, and comprehensive approach to untargeted milk analysis. These inherent strengths of NMR make it a formidable complementary tool to mass spectrometry-based techniques in milk metabolomic studies. This review aims to provide a comprehensive overview of the applications of NMR techniques in the quality assessment and authentication of bovine milk. It will focus on the experimental setup and data processing techniques that contribute to achieving accurate and highly reproducible results. The review will also highlight key studies that have utilized commonly used NMR methodologies in milk analysis, covering a wide range of application fields. These applications include determining milk animal species and feeding regimes, as well as assessing milk nutritional quality and authenticity. By providing an overview of the diverse applications of NMR in milk analysis, this review aims to demonstrate the versatility and significance of NMR spectroscopy as an invaluable tool for milk and dairy metabolomics research and hence, for assessing the quality and authenticity of bovine milk.
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Affiliation(s)
- Dilek Eltemur
- Laimburg Research Centre, Laimburg 6—Pfatten (Vadena), 39040 Auer, Italy (A.C.)
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Piazza Unversità 5, 39100 Bolzano, Italy
| | - Peter Robatscher
- Laimburg Research Centre, Laimburg 6—Pfatten (Vadena), 39040 Auer, Italy (A.C.)
| | - Michael Oberhuber
- Laimburg Research Centre, Laimburg 6—Pfatten (Vadena), 39040 Auer, Italy (A.C.)
| | - Matteo Scampicchio
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Piazza Unversità 5, 39100 Bolzano, Italy
| | - Alberto Ceccon
- Laimburg Research Centre, Laimburg 6—Pfatten (Vadena), 39040 Auer, Italy (A.C.)
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Purroy F, Ois A, Jove M, Arque G, Sol J, Mauri-Capdevila G, Rodriguez-Campello A, Pamplona R, Portero M, Roquer J. Lipidomic signature of stroke recurrence after transient ischemic attack. Sci Rep 2023; 13:13706. [PMID: 37607967 PMCID: PMC10444771 DOI: 10.1038/s41598-023-40838-7] [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: 12/27/2022] [Accepted: 08/17/2023] [Indexed: 08/24/2023] Open
Abstract
While TIA patients have transient symptoms, they should not be underestimated, as they could have an underlying pathology that may lead to a subsequent stroke: stroke recurrence (SR). Previously, it has been described the involvement of lipids in different vascular diseases. The aim of the current study was to perform a lipidomic analysis to identify differences in the lipidomic profile between patients with SR and patients without. Untargeted lipidomic analysis was performed in plasma samples of 460 consecutive TIA patients recruited < 24 h after the onset of symptoms. 37 (8%) patients suffered SR at 90 days. Lipidomic profiling disclosed 7 lipid species differentially expressed between groups: 5 triacylglycerides (TG), 1 diacylglyceride (DG), and 1 alkenyl-PE (plasmalogen) [specifically, TG(56:1), TG(63:0), TG(58:2), TG(50:5), TG(53:7, DG(38:5)) and PE(P-18:0/18:2)]. 6 of these 7 lipid species belonged to the glycerolipid family and a plasmalogen, pointing to bioenergetics pathways, as well as oxidative stress response. In this context, it was proposed the PE(P-18:0/18:2) as potential biomarker of SR condition.The observed changes in lipid patterns suggest pathophysiological mechanisms associated with lipid droplets metabolism and antioxidant protection that is translated to plasma level as consequence of a more intensive or high-risk ischemic condition related to SR.
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Affiliation(s)
- F Purroy
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain.
- Stroke Unit, Department of Neurology, Universitat de Lleida, Hospital Universitari Arnau de Vilanova, Avda Rovira Roure 80, 25198, Lleida, Spain.
| | - A Ois
- Department of Neurology, Neurology Neurovascular Research Unit Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - M Jove
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Spain
| | - G Arque
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain
| | - J Sol
- Institut Català de la Salut (ICS), Atenció Primària, Lleida, Spain
- Research Support Unit Lleida, Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Lleida, Spain
| | - G Mauri-Capdevila
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain
- Stroke Unit, Department of Neurology, Universitat de Lleida, Hospital Universitari Arnau de Vilanova, Avda Rovira Roure 80, 25198, Lleida, Spain
| | - A Rodriguez-Campello
- Department of Neurology, Neurology Neurovascular Research Unit Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - R Pamplona
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Spain
| | - M Portero
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Spain
| | - J Roquer
- Department of Neurology, Neurology Neurovascular Research Unit Hospital del Mar Research Institute (IMIM), Barcelona, Spain
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Speziale R, Montesano C, Di Pietro G, Cicero DO, Summa V, Monteagudo E, Orsatti L. The Urine Metabolome of R6/2 and zQ175DN Huntington's Disease Mouse Models. Metabolites 2023; 13:961. [PMID: 37623904 PMCID: PMC10456449 DOI: 10.3390/metabo13080961] [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: 07/17/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Huntington's disease (HD) is caused by the expansion of a polyglutamine (polyQ)-encoding tract in exon 1 of the huntingtin gene to greater than 35 CAG repeats. It typically has a disease course lasting 15-20 years, and there are currently no disease-modifying therapies available. Thus, there is a need for faithful mouse models of HD to use in preclinical studies of disease mechanisms, target validation, and therapeutic compound testing. A large variety of mouse models of HD were generated, none of which fully recapitulate human disease, complicating the selection of appropriate models for preclinical studies. Here, we present the urinary liquid chromatography-high-resolution mass spectrometry analysis employed to identify metabolic alterations in transgenic R6/2 and zQ175DN knock-in mice. In R6/2 mice, the perturbation of the corticosterone metabolism and the accumulation of pyrraline, indicative of the development of insulin resistance and the impairment of pheromone excretion, were observed. Differently from R6/2, zQ175DN mice showed the accumulation of oxidative stress metabolites. Both genotypes showed alterations in the tryptophan metabolism. This approach aims to improve our understanding of the molecular mechanisms involved in HD neuropathology, facilitating the selection of appropriate mouse models for preclinical studies. It also aims to identify potential biomarkers specific to HD.
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Affiliation(s)
- Roberto Speziale
- Experimental Pharmacology Department, IRBM SpA, Via Pontina km 30.600, 00071 Pomezia, Italy;
| | - Camilla Montesano
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy;
| | - Giulia Di Pietro
- Department of Chemical Sciences and Technology, University of Rome “Tor Vergata”, Via Cracovia 50, 00133 Roma, Italy; (G.D.P.); (D.O.C.)
| | - Daniel Oscar Cicero
- Department of Chemical Sciences and Technology, University of Rome “Tor Vergata”, Via Cracovia 50, 00133 Roma, Italy; (G.D.P.); (D.O.C.)
| | - Vincenzo Summa
- Department of Pharmacy, University of Napoli “Federico II”, Corso Umberto I 40, 80138 Napoli, Italy;
| | - Edith Monteagudo
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, CA 90045, USA;
| | - Laura Orsatti
- Experimental Pharmacology Department, IRBM SpA, Via Pontina km 30.600, 00071 Pomezia, Italy;
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Kumar BS. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) in disease diagnosis: an overview. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:3768-3784. [PMID: 37503728 DOI: 10.1039/d3ay00867c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tissue analysis, which is essential to histology and is considered the benchmark for the diagnosis and prognosis of many illnesses, including cancer, is significant. During surgery, the surgical margin of the tumor is assessed using the labor-intensive, challenging, and commonly subjective technique known as frozen section histopathology. In the biopsy section, large numbers of molecules can now be visualized at once (ion images) following recent developments in [MSI] mass spectrometry imaging under atmospheric conditions. This is vastly superior to and different from the single optical tissue image processing used in traditional histopathology. This review article will focus on the advancement of desorption electrospray ionization mass spectrometry imaging [DESI-MSI] technique, which is label-free and requires little to no sample preparation. Since the proportion of molecular species in normal and abnormal tissues is different, DESI-MSI can capture ion images of the distributions of lipids and metabolites on biopsy sections, which can provide rich diagnostic information. This is not a systematic review but a summary of well-known, cutting-edge and recent DESI-MSI applications in cancer research between 2018 and 2023.
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Affiliation(s)
- Bharath Sampath Kumar
- Independent Researcher, 21, B2, 27th Street, Nanganallur, Chennai 61, TamilNadu, India.
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O'Connor LM, O'Connor BA, Lim SB, Zeng J, Lo CH. Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective. J Pharm Anal 2023; 13:836-850. [PMID: 37719197 PMCID: PMC10499660 DOI: 10.1016/j.jpha.2023.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/19/2023] Open
Abstract
Bioinformatic analysis of large and complex omics datasets has become increasingly useful in modern day biology by providing a great depth of information, with its application to neuroscience termed neuroinformatics. Data mining of omics datasets has enabled the generation of new hypotheses based on differentially regulated biological molecules associated with disease mechanisms, which can be tested experimentally for improved diagnostic and therapeutic targeting of neurodegenerative diseases. Importantly, integrating multi-omics data using a systems bioinformatics approach will advance the understanding of the layered and interactive network of biological regulation that exchanges systemic knowledge to facilitate the development of a comprehensive human brain profile. In this review, we first summarize data mining studies utilizing datasets from the individual type of omics analysis, including epigenetics/epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, and spatial omics, pertaining to Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We then discuss multi-omics integration approaches, including independent biological integration and unsupervised integration methods, for more intuitive and informative interpretation of the biological data obtained across different omics layers. We further assess studies that integrate multi-omics in data mining which provide convoluted biological insights and offer proof-of-concept proposition towards systems bioinformatics in the reconstruction of brain networks. Finally, we recommend a combination of high dimensional bioinformatics analysis with experimental validation to achieve translational neuroscience applications including biomarker discovery, therapeutic development, and elucidation of disease mechanisms. We conclude by providing future perspectives and opportunities in applying integrative multi-omics and systems bioinformatics to achieve precision phenotyping of neurodegenerative diseases and towards personalized medicine.
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Affiliation(s)
- Lance M. O'Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Blake A. O'Connor
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
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Bellot PENR, Braga ES, Omage FB, da Silva Nunes FL, Lima SCVC, Lyra CO, Marchioni DML, Pedrosa LFC, Barbosa F, Tasic L, Sena-Evangelista KCM. Plasma lipid metabolites as potential biomarkers for identifying individuals at risk of obesity-induced metabolic complications. Sci Rep 2023; 13:11729. [PMID: 37474543 PMCID: PMC10359283 DOI: 10.1038/s41598-023-38703-8] [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: 12/28/2022] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
Lipidomics studies have indicated an association between obesity and lipid metabolism dysfunction. This study aimed to evaluate and compare cardiometabolic risk factors, and the lipidomic profile in adults and older people. A cross-sectional study was conducted with 72 individuals, divided into two sex and age-matched groups: obese (body mass index-BMI ≥ 30 kg/m2; n = 36) and non-obese (BMI < 30 kg/m2; n = 36). The lipidomic profiles were evaluated in plasma using 1H nuclear magnetic resonance (1H-NMR) spectroscopy. Obese individuals had higher waist circumference (p < 0.001), visceral adiposity index (p = 0.029), homeostatic model assessment insulin resistance (HOMA-IR) (p = 0.010), and triacylglycerols (TAG) levels (p = 0.018). 1H-NMR analysis identified higher amounts of saturated lipid metabolite fragments, lower levels of unsaturated lipids, and some phosphatidylcholine species in the obese group. Two powerful machine learning (ML) models-k-nearest neighbors (kNN) and XGBoost (XGB) were employed to characterize the lipidomic profile of obese individuals. The results revealed metabolic alterations associated with obesity in the NMR signals. The models achieved high accuracy of 86% and 81%, respectively. The feature importance analysis identified signal at 1.50-1.60 ppm (-CO-CH2-CH2-, Cholesterol and fatty acid in TAG, Phospholipids) to have the highest importance in the two models.
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Affiliation(s)
- Paula Emília Nunes Ribeiro Bellot
- Postgraduate Program in Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Erik Sobrinho Braga
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | - Francisca Leide da Silva Nunes
- Postgraduate Program in Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Clélia Oliveira Lyra
- Department of Nutrition, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Dirce Maria Lobo Marchioni
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo Campus, São Paulo, SP, Brazil
| | | | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ljubica Tasic
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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49
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Chen CL, Chen YT, Liao WY, Chang YS, Yu JS, Juo BR. Urinary Metabolomic Analysis of Prostate Cancer by UPLC-FTMS and UPLC-Ion Trap MS n. Diagnostics (Basel) 2023; 13:2270. [PMID: 37443661 DOI: 10.3390/diagnostics13132270] [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: 05/31/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Accumulative evidence suggests metabolic disorders correlate with prostate cancer. Metabolic profiling of urine allows the measurement of numerous metabolites simultaneously. This study set up a metabolomic platform consisting of UPLC-FTMS and UPLC-ion trap MSn for urine metabolome analysis. The platform improved retention time, mass accuracy, and signal stability. Additionally, the product ion spectrum obtained from ion trap MSn facilitated structure elucidation of candidate metabolites, especially when authentic standards were not available. Urine samples from six hernia patients and six BPH patients were used for the initial establishment of the analytic platform. This platform was further employed to analyze the urine samples of 27 PCa and 49 BPH patients. Choosing the upper and lower 16% of metabolites, 258 metabolite candidates were selected. Twenty-four of them with AUC values larger than 0.65 were further selected. Eighteen of the twenty-four features can be matched in METLIN and HMDB. Eleven of the eighteen features can be interpreted by MSn experiments. They were used for the combination achieving the best differential power. Finally, four metabolites were combined to reach the AUC value of 0.842 (CI 95, 0.7559 to 0.9279). This study demonstrates the urinary metabolomic analysis of prostate cancer and sheds light on future research.
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Affiliation(s)
- Chien-Lun Chen
- Molecular Medicine Research Center, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
- Department of Urology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kwei-San, Taoyuan 33305, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Wen-Yu Liao
- Molecular Medicine Research Center, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
| | - Bao-Rong Juo
- Molecular Medicine Research Center, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
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Ross IL, Beardslee JA, Steil MM, Chihanga T, Kennedy MA. Statistical considerations and database limitations in NMR-based metabolic profiling studies. Metabolomics 2023; 19:64. [PMID: 37378680 DOI: 10.1007/s11306-023-02027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Interpretation and analysis of NMR-based metabolic profiling studies is limited by substantially incomplete commercial and academic databases. Statistical significance tests, including p-values, VIP scores, AUC values and FC values, can be largely inconsistent. Data normalization prior to statistical analysis can cause erroneous outcomes. OBJECTIVES The objectives were (1) to quantitatively assess consistency among p-values, VIP scores, AUC values and FC values in representative NMR-based metabolic profiling datasets, (2) to assess how data normalization can impact statistical significance outcomes, (3) to determine resonance peak assignment completion potential using commonly used databases and (4) to analyze intersection and uniqueness of metabolite space in these databases. METHODS P-values, VIP scores, AUC values and FC values, and their dependence on data normalization, were determined in orthotopic mouse model of pancreatic cancer and two human pancreatic cancer cell lines. Completeness of resonance assignments were evaluated using Chenomx, the human metabolite database (HMDB) and the COLMAR database. The intersection and uniqueness of the databases was quantified. RESULTS P-values and AUC values were strongly correlated compared to VIP or FC values. Distributions of statistically significant bins depended strongly on whether or not datasets were normalized. 40-45% of peaks had either no or ambiguous database matches. 9-22% of metabolites were unique to each database. CONCLUSIONS Lack of consistency in statistical analyses of metabolomics data can lead to misleading or inconsistent interpretation. Data normalization can have large effects on statistical analysis and should be justified. About 40% of peak assignments remain ambiguous or impossible with current databases. 1D and 2D databases should be made consistent to maximize metabolite assignment confidence and validation.
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Affiliation(s)
- Imani L Ross
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, 92093, USA
| | - Julie A Beardslee
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Maria M Steil
- Division of Plastic Surgery, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Tafadzwa Chihanga
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
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