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Covarrubias C, Cammisotto PG, Shamout S, Campeau L. Decrease in the Ratio proBDNF/BDNF in the Urine of Aging Female Patients with OAB. Metabolites 2023; 13:723. [PMID: 37367881 DOI: 10.3390/metabo13060723] [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: 05/04/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
Imbalance in the levels of neurotrophins, growth factors crucial in the development, function, and survival of neurons is commonly observed in many pathological states. Concentrations of brain-derived neurotrophic factor (BDNF) and its precursor (proBDNF) were measured in the urine of a cohort of aging female patients with overactive bladder disease (OAB). When reported to creatinine, levels were similar between OAB patients and healthy controls. However, the ratio proBDNF/BDNF was significantly decreased in the OAB group. Receiver operating characteristic (ROC) curve analysis of the ratio proBDNF/BDNF displayed a good diagnostic value for OAB (AUC = 0.729). Clinical questionnaires of symptom severity (OABSS and IIQ-7) were negatively correlated with this ratio. On the other hand, microRNAs (miRNA) involved in proBDNF gene translation were expressed at comparable levels between groups. However, urinary enzymatic activity of matrix metalloproteinase-9 (MMP-9), the enzyme that cleaves proBDNF into BDNF, was increased in OAB compared to controls. Levels of miR-491-5p, the main miRNA that downregulates MMP-9 synthesis, were greatly decreased in urine from OAB patients. These results suggest that the ratio proBDNF/BDNF could be useful in the phenotyping of OAB in an aging population, and the difference could originate from enhanced MMP-9 enzymatic activity rather than translational control.
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Affiliation(s)
| | | | - Samer Shamout
- Lady Davis Institute, McGill University, Montreal, QC H3A 0G4, Canada
| | - Lysanne Campeau
- Lady Davis Institute, McGill University, Montreal, QC H3A 0G4, Canada
- Urology Department, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
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Ferrante L, Rajpoot K, Jeeves M, Ludwig C. Automated analysis for multiplet identification from ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. Wellcome Open Res 2023; 7:262. [PMID: 37008249 PMCID: PMC10050905 DOI: 10.12688/wellcomeopenres.18248.2] [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] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D- 1H, 13C-HSQC NMR spectra arising from 13C - 13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D- 1H, 13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
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Affiliation(s)
- Laura Ferrante
- School of Computer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kashif Rajpoot
- University of Birmingham Dubai, Dubai International Academic City, United Arab Emirates
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK
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Liu Y, Li S, Feng Y, Zhang Y, Ouyang J, Li S, Wang J, Tan L, Zou L. Serum metabolomic analyses reveal the potential metabolic biomarkers for prediction of amatoxin poisoning. Toxicon 2023; 230:107153. [PMID: 37178797 DOI: 10.1016/j.toxicon.2023.107153] [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: 03/06/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Amatoxin poisoning leads to over 90% of deaths in mushroom poisoning. The objective of present study was to identify the potential metabolic biomarkers for early diagnosis of amatoxin poisoning. Serum samples were collected from 61 patients with amatoxin poisoning and 61 healthy controls. An untargeted metabolomics analysis was performed using the ultra-high-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS/MS). Multivariate statistical analysis revealed that the patients with amatoxin poisoning could be clearly separated from healthy controls on the basis of their metabolic fingerprints. There were 33 differential metabolites including 15 metabolites up-regulated metabolites and 18 down-regulated metabolites in patients with amatoxin poisoning compared to healthy controls. These metabolites mainly enriched in the lipid metabolism and amino acid metabolism pathways, such as Glycerophospholipid metabolism, Sphingolipid metabolism, Phenylalanine tyrosine and typtophan biosynthesis, Tyrosine metabolism, Arginine and proline metabolism, which may serve important roles in the amatoxin poisoning. Among the differential metabolites, a total of 8 significant metabolic markers were identified for discriminating patients with amatoxin poisoning from healthy controls, including Glycochenodeoxycholate-3-sulfate (GCDCA-S), 11-Oxo-androsterone glucuronide, Neomenthol-glucuronide, Dehydroisoandrosterone 3-glucuronide, Glucose 6-phosphate (G6P), Lanthionine ketimine, Glycerophosphocholine (GPC) and Nicotinamide ribotide, which achieved satisfactory diagnostic accuracy (AUC>0.8) in both discovery and validation cohorts. Strikingly, the Pearson's correlation analysis indicated that 11-Oxo-androsterone glucuronide, G6P and GCDCA-S were positively correlated with the liver injury induced by amatoxin poisoning. The findings of the current study may provide insight into the pathological mechanism of amatoxin poisoning and screened out the reliable metabolic biomarkers to contribute the clinical early diagnosis of amatoxin poisoning.
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Affiliation(s)
- Yarong Liu
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410013, PR China; Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, No. 371 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Shumei Li
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410013, PR China; Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, No. 371 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Yang Feng
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410013, PR China; Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, No. 371 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Yiyuan Zhang
- Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China
| | - Jielin Ouyang
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410013, PR China; Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, No. 371 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Shutong Li
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410013, PR China; Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, No. 371 Tongzipo Road, Changsha, Hunan, 410013, PR China
| | - Jia Wang
- Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China.
| | - Lihong Tan
- Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China.
| | - Lianhong Zou
- Institute of Clinical Translational Medicine, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, No. 371 Tongzipo Road, Changsha, Hunan, 410013, PR China.
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Ferreira RS, Ribeiro PR, Silva JHCE, Hoppe JB, de Almeida MMA, de Lima Ferreira BC, Andrade GB, de Souza SB, Ferdandez LG, de Fátima Dias Costa M, Salbego CG, Rivera AD, Longoni A, de Assis AM, Pieropan F, Moreira JCF, Costa SL, Butt AM, da Silva VDA. Amburana cearensis seed extract stimulates astrocyte glutamate homeostatic mechanisms in hippocampal brain slices and protects oligodendrocytes against ischemia. BMC Complement Med Ther 2023; 23:154. [PMID: 37170258 PMCID: PMC10173544 DOI: 10.1186/s12906-023-03959-0] [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: 09/27/2022] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Stroke is a leading cause of death and disability worldwide. A major factor in brain damage following ischemia is excitotoxicity caused by elevated levels of the neurotransmitter glutamate. In the brain, glutamate homeostasis is a primary function of astrocytes. Amburana cearensis has long been used in folk medicine and seed extract obtained with dichloromethane (EDAC) have previously been shown to exhibit cytoprotective activity in vitro. The aim of the present study was to analyse the activity of EDAC in hippocampal brain slices. METHODS We prepared a dichloromethane extract (EDAC) from A. cearensis seeds and characterized the chemical constituents by 1H and 13C-NMR. Hippocampal slices from P6-8 or P90 Wistar rats were used for cell viability assay or glutamate uptake test. Hippocampal slices from P10-12 transgenic mice SOX10-EGFP and GFAP-EGFP and immunofluorescence for GS, GLAST and GLT1 were used to study oligodendrocytes and astrocytes. RESULTS Astrocytes play a critical role in glutamate homeostasis and we provide immunohistochemical evidence that in excitotoxicity EDAC increased expression of glutamate transporters and glutamine synthetase, which is essential for detoxifying glutamate. Next, we directly examined astrocytes using transgenic mice in which glial fibrillary acidic protein (GFAP) drives expression of enhanced green fluorescence protein (EGFP) and show that glutamate excitotoxicity caused a decrease in GFAP-EGFP and that EDAC protected against this loss. This was examined further in the oxygen-glucose deprivation (OGD) model of ischemia, where EDAC caused an increase in astrocytic process branching, resulting in an increase in GFAP-EGFP. Using SOX10-EGFP reporter mice, we show that the acute response of oligodendrocytes to OGD in hippocampal slices is a marked loss of their processes and EDAC protected oligodendrocytes against this damage. CONCLUSION This study provides evidence that EDAC is cytoprotective against ischemia and glutamate excitotoxicity by modulating astrocyte responses and stimulating their glutamate homeostatic mechanisms.
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Affiliation(s)
- Rafael Short Ferreira
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK
| | - Paulo Roberto Ribeiro
- Metabolomics Research Group, Department of Organic Chemistry, Chemistry Institute, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Juliana Helena Castro E Silva
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK
| | - Juliana Bender Hoppe
- Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Monique Marylin Alves de Almeida
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK
| | - Beatriz Correia de Lima Ferreira
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
| | - Gustavo Borges Andrade
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
| | - Suzana Braga de Souza
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
| | - Luzimar Gonzaga Ferdandez
- Biochemistry, Biotechnology and Bioproducts Laboratory, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Maria de Fátima Dias Costa
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil
| | - Christianne Gazzana Salbego
- Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Andrea Domenico Rivera
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK
| | - Aline Longoni
- Health Sciences Centre, Post-Graduate Program in Health and Behaviour, Catholic University of Pelotas, Pelotas, Brazil
| | - Adriano Martimbianco de Assis
- Health Sciences Centre, Post-Graduate Program in Health and Behaviour, Catholic University of Pelotas, Pelotas, Brazil
| | - Francesca Pieropan
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK
| | - José Cláudio Fonseca Moreira
- Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Silvia Lima Costa
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil.
| | - Arthur Morgan Butt
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK.
| | - Victor Diogenes Amaral da Silva
- Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia - UFBA, Salvador, Bahia, 40110-902, Brazil.
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth, PO1 2DT, UK.
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Wissenbach DK, Steuer AE. Advances in testing for sample manipulation in clinical and forensic toxicology - Part A: urine samples. Anal Bioanal Chem 2023:10.1007/s00216-023-04711-w. [PMID: 37145190 PMCID: PMC10404192 DOI: 10.1007/s00216-023-04711-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023]
Abstract
In many countries, adherence testing is used to monitor consumption behavior or to prove abstinence. Urine and hair are most commonly used, although other biological fluids are available. Positive test results are usually associated with serious legal or economic consequences. Therefore, various sample manipulation and adulteration strategies are used to circumvent such a positive result. In these critical review articles on sample adulteration of urine (part A) and hair samples (part B) in the context of clinical and forensic toxicology, recent trends and strategies to improve sample adulteration and manipulation testing published in the past 10 years are described and discussed. Typical manipulation and adulteration strategies include undercutting the limits of detection/cut-off by dilution, substitution, and adulteration. New or alternative strategies for detecting sample manipulation attempts can be generally divided into improved detection of established urine validity markers and direct and indirect techniques or approaches to screening for new adulteration markers. In this part A of the review article, we focused on urine samples, where the focus in recent years has been on new (in)direct substitution markers, particularly for synthetic (fake) urine. Despite various and promising advances in detecting manipulation, it remains a challenge in clinical and forensic toxicology, and simple, reliable, specific, and objective markers/techniques are still lacking, for example, for synthetic urine.
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Affiliation(s)
- Dirk K Wissenbach
- Institute of Forensic Medicine, Jena University Hospital, Jena, Germany
| | - Andrea E Steuer
- Department of Forensic Pharmacology & Toxicology, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland.
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56
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Wang D, Gao Y, Li Y, Zhao Y, Du X, Li X, Zhang Y, Liu S, Xu Y. Plasma metabolomics and network pharmacology identified glutamate, glutamine, and arginine as biomarkers of depression under Shuganjieyu capsule treatment. J Pharm Biomed Anal 2023; 232:115419. [PMID: 37146496 DOI: 10.1016/j.jpba.2023.115419] [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: 01/17/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/07/2023]
Abstract
Depression is a psychiatric disorder and confers an enormous burden on society. Mild to moderate forms of depression (MMD) are particularly common. Our previous studies showed that the Shuganjieyu (SGJY) capsule might improve depressive and cognitive symptoms in patients with MMD. However, biomarkers evaluating the efficacy of SGJY and the underlying mechanism remains unclear. The aim of the present study was to discover efficacy biomarkers and explore the underlying mechanisms of SGJY as antidepression treatment. Twenty-three patients with MMD were recruited and administered with SGJY for 8 weeks. Results showed that the content of 19 metabolites changed significantly in the plasma of patients with MMD, among which 8 metabolites improved significantly after SGJY treatment. Network pharmacology analysis showed that 19 active compounds, 102 potential targets, and 73 enzymes were related to the mechanistic action of SGJY. Through a comprehensive analysis, we identified four hub enzymes (GLS2, GLS, GLUL, and ADC), three key differential metabolites (glutamine, glutamate, and arginine), and two shared pathways (alanine, aspartate, and glutamate metabolism; and arginine biosynthesis). Receiver operating characteristic curve (ROC) analysis showed that the three metabolites had a high diagnostic ability. The expression of hub enzymes was validated using RT-qPCR in animal models. Overall, glutamate, glutamine, and arginine may be potential biomarkers for evaluating the efficacy of SGJY. The present study provides a new strategy for pharmacodynamic evaluation and mechanistic study of SGJY, and offers new information for clinical practice and treatment research.
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Affiliation(s)
- Dan Wang
- Basic Medical College, Shanxi Medical University, 030000 Taiyuan, China; Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yao Gao
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yaojun Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yu Zhao
- Basic Medical College, Shanxi Medical University, 030000 Taiyuan, China; Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Xinzhe Du
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Xinrong Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yu Zhang
- Basic Medical College, Shanxi Medical University, 030000 Taiyuan, China
| | - Sha Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China.
| | - Yong Xu
- Department of Psychiatry, Taiyuan Central Hospital of Shanxi Medical University, 030032 Taiyuan, China; Department of Psychiatry, First Clinical Medical College of Shanxi Medical University, 030001 Taiyuan, China.
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Heynen JP, McHugh RR, Boora NS, Simcock G, Kildea S, Austin MP, Laplante DP, King S, Montina T, Metz GAS. Urinary 1H NMR Metabolomic Analysis of Prenatal Maternal Stress Due to a Natural Disaster Reveals Metabolic Risk Factors for Non-Communicable Diseases: The QF2011 Queensland Flood Study. Metabolites 2023; 13:metabo13040579. [PMID: 37110237 PMCID: PMC10145263 DOI: 10.3390/metabo13040579] [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: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Prenatal stress alters fetal programming, potentially predisposing the ensuing offspring to long-term adverse health outcomes. To gain insight into environmental influences on fetal development, this QF2011 study evaluated the urinary metabolomes of 4-year-old children (n = 89) who were exposed to the 2011 Queensland flood in utero. Proton nuclear magnetic resonance spectroscopy was used to analyze urinary metabolic fingerprints based on maternal levels of objective hardship and subjective distress resulting from the natural disaster. In both males and females, differences were observed between high and low levels of maternal objective hardship and maternal subjective distress groups. Greater prenatal stress exposure was associated with alterations in metabolites associated with protein synthesis, energy metabolism, and carbohydrate metabolism. These alterations suggest profound changes in oxidative and antioxidative pathways that may indicate a higher risk for chronic non-communicable diseases such obesity, insulin resistance, and diabetes, as well as mental illnesses, including depression and schizophrenia. Thus, prenatal stress-associated metabolic biomarkers may provide early predictors of lifetime health trajectories, and potentially serve as prognostic markers for therapeutic strategies in mitigating adverse health outcomes.
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Affiliation(s)
- Joshua P Heynen
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Southern Alberta Genome Sciences Centre, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Rebecca R McHugh
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Naveenjyote S Boora
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Gabrielle Simcock
- Midwifery Research Unit, Mater Research Institute, University of Queensland, Brisbane, QLD 4072, Australia
- School of Psychology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Sue Kildea
- Midwifery Research Unit, Mater Research Institute, University of Queensland, Brisbane, QLD 4072, Australia
- Molly Wardaguga Research Centre, Faculty of Health, Charles Darwin University, Alice Springs, NT 0870, Australia
| | - Marie-Paule Austin
- Perinatal and Woman's Health Unit, University of New South Wales, Sydney, NSW 2052, Australia
| | - David P Laplante
- Centre for Child Development and Mental Health, Lady Davis Institute for Medical Research, Jewish General Hospital, 4335 Chemin de la Côte-Sainte-Catherine, Montreal, QC H3T 1E4, Canada
| | - Suzanne King
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Boulevard, Montreal, QC H4H 1R3, Canada
| | - Tony Montina
- Southern Alberta Genome Sciences Centre, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Gerlinde A S Metz
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Southern Alberta Genome Sciences Centre, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
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Chen Ming Low J, Wright AJ, Hesse F, Cao J, Brindle KM. Metabolic imaging with deuterium labeled substrates. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:39-51. [PMID: 37321757 DOI: 10.1016/j.pnmrs.2023.02.002] [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: 01/06/2023] [Revised: 01/12/2023] [Accepted: 02/07/2023] [Indexed: 06/17/2023]
Abstract
Deuterium metabolic imaging (DMI) is an emerging clinically-applicable technique for the non-invasive investigation of tissue metabolism. The generally short T1 values of 2H-labeled metabolites in vivo can compensate for the relatively low sensitivity of detection by allowing rapid signal acquisition in the absence of significant signal saturation. Studies with deuterated substrates, including [6,6'-2H2]glucose, [2H3]acetate, [2H9]choline and [2,3-2H2]fumarate have demonstrated the considerable potential of DMI for imaging tissue metabolism and cell death in vivo. The technique is evaluated here in comparison with established metabolic imaging techniques, including PET measurements of 2-deoxy-2-[18F]fluoro-d-glucose (FDG) uptake and 13C MR imaging of the metabolism of hyperpolarized 13C-labeled substrates.
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Affiliation(s)
- Jacob Chen Ming Low
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Alan J Wright
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Friederike Hesse
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Jianbo Cao
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
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Miller WM, Ziegler KM, Yilmaz A, Saiyed N, Ustun I, Akyol S, Idler J, Sims MD, Maddens ME, Graham SF. Association of Metabolomic Biomarkers with Sleeve Gastrectomy Weight Loss Outcomes. Metabolites 2023; 13:metabo13040506. [PMID: 37110164 PMCID: PMC10145663 DOI: 10.3390/metabo13040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
This prospective observational study aimed to evaluate the association of metabolomic alterations with weight loss outcomes following sleeve gastrectomy (SG). We evaluated the metabolomic profile of serum and feces prior to SG and three months post-SG, along with weight loss outcomes in 45 adults with obesity. The percent total weight loss for the highest versus the lowest weight loss tertiles (T3 vs. T1) was 17.0 ± 1.3% and 11.1 ± 0.8%, p < 0.001. Serum metabolite alterations specific to T3 at three months included a decrease in methionine sulfoxide concentration as well as alterations to tryptophan and methionine metabolism (p < 0.03). Fecal metabolite changes specific to T3 included a decrease in taurine concentration and perturbations to arachidonic acid metabolism, and taurine and hypotaurine metabolism (p < 0.002). Preoperative metabolites were found to be highly predictive of weight loss outcomes in machine learning algorithms, with an average area under the curve of 94.6% for serum and 93.4% for feces. This comprehensive metabolomics analysis of weight loss outcome differences post-SG highlights specific metabolic alterations as well as machine learning algorithms predictive of weight loss. These findings could contribute to the development of novel therapeutic targets to enhance weight loss outcomes after SG.
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Affiliation(s)
- Wendy M. Miller
- Department of Nutrition and Preventive Medicine, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA
- Oakland University William Beaumont School of Medicine, 586 Pioneer Dr, Rochester, MI 48309, USA
| | - Kathryn M. Ziegler
- Department of Nutrition and Preventive Medicine, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA
- Oakland University William Beaumont School of Medicine, 586 Pioneer Dr, Rochester, MI 48309, USA
| | - Ali Yilmaz
- Beaumont Research Institute, 3811 W 13 Mile Rd, Royal Oak, MI 48073, USA
| | - Nazia Saiyed
- Beaumont Research Institute, 3811 W 13 Mile Rd, Royal Oak, MI 48073, USA
| | - Ilyas Ustun
- DePaul University Jarvis College of Computing and Digital Media, 243 S Wabash Ave, Chicago, IL 60604, USA
| | - Sumeyya Akyol
- NX Prenatal Inc. Laboratory, 4800 Fournace Place, Suite BW28, Bellaire, TX 77401, USA
| | - Jay Idler
- Allegheny Health Network, West Penn Hospital, 4815 Liberty Ave, Suite GR50, Pittsburgh, PA 15224, USA
- Drexel University College of Medicine, 2900 W Queen Ln, Philadelphia, PA 19129, USA
| | - Matthew D. Sims
- Department of Nutrition and Preventive Medicine, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA
- Beaumont Research Institute, 3811 W 13 Mile Rd, Royal Oak, MI 48073, USA
| | - Michael E. Maddens
- Department of Nutrition and Preventive Medicine, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA
- Oakland University William Beaumont School of Medicine, 586 Pioneer Dr, Rochester, MI 48309, USA
| | - Stewart F. Graham
- Department of Nutrition and Preventive Medicine, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA
- Beaumont Research Institute, 3811 W 13 Mile Rd, Royal Oak, MI 48073, USA
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Chen C, Kim RH, Hwang KT, Kim J. Chemical compounds and bioactivities of the extracts from radish (Raphanus sativus) sprouts exposed to red and blue light-emitting diodes during cultivation. Eur Food Res Technol 2023. [DOI: 10.1007/s00217-023-04235-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Ito Y, Uda S, Kokaji T, Hirayama A, Soga T, Suzuki Y, Kuroda S, Kubota H. Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures. Sci Rep 2023; 13:4758. [PMID: 36959243 PMCID: PMC10036622 DOI: 10.1038/s41598-023-31547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
Interactions between various molecular species in biological phenomena give rise to numerous networks. The investigation of these networks, including their statistical and biochemical interactions, supports a deeper understanding of biological phenomena. The clustering of nodes associated with molecular species and enrichment analysis is frequently applied to examine the biological significance of such network structures. However, these methods focus on delineating the function of a node. As such, in-depth investigations of the edges, which are the connections between the nodes, are rarely explored. In the current study, we aimed to investigate the functions of the edges rather than the nodes. To accomplish this, for each network, we categorized the edges and defined the edge type based on their biological annotations. Subsequently, we used the edge type to compare the network structures of the metabolome and transcriptome in the livers of healthy (wild-type) and obese (ob/ob) mice following oral glucose administration (OGTT). The findings demonstrate that the edge type can facilitate the characterization of the state of a network structure, thereby reducing the information available through datasets containing the OGTT response in the metabolome and transcriptome.
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Affiliation(s)
- Yuki Ito
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Toshiya Kokaji
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5, Takayamacho, Ikoma, Nara, 630-0192, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Shinya Kuroda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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Fernández S, Castro R, López-Radcenco A, Rodriguez P, Carrera I, García-Carnelli C, Moyna G. Beyond cannabinoids: Application of NMR-based metabolomics for the assessment of Cannabis sativa L. crop health. FRONTIERS IN PLANT SCIENCE 2023; 14:1025932. [PMID: 37035042 PMCID: PMC10075229 DOI: 10.3389/fpls.2023.1025932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
While Cannabis sativa L. varieties have been traditionally characterized by their major cannabinoid profile, it is now well established that other plant metabolites can also have physiological effects, including minor cannabinoids, terpenes, and flavonoids. Given the multiple applications of cannabis in the medical field, it is therefore critical to characterize it according to its chemical composition (i.e., its metabolome) and not only its botanical traits. With this in mind, the cannabinoid and metabolomic profiles from inflorescences of two C. sativa varieties with either high Δ9-tetrahydrocannabinolic acid (THCA) or high cannabidiolic acid (CBDA) contents harvested at different times were studied. According to results from HPLC and NMR-based untargeted metabolomic analyses of organic and aqueous plant material extracts, we show that in addition to expected variations according to cannabinoid profiles, it is possible to distinguish between harvests of the same variety. In particular, it was possible to correlate variations in the metabolome with presence of powdery mildew, leading to the identification of molecular markers associated with this fungal infection in C. sativa.
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Affiliation(s)
- Santiago Fernández
- Laboratorio de Farmacognosia y Productos Naturales, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Rossina Castro
- Laboratorio de Farmacognosia y Productos Naturales, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Andrés López-Radcenco
- Laboratorio de Fisicoquímica Orgánica, Departamento de Química del Litoral, Centro Universitario Regional Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Paula Rodriguez
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica and Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Inés Carrera
- Laboratorio de Experimentación Animal – Área Farmacología, Departamento de Ciencias Farmacéuticas, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Carlos García-Carnelli
- Laboratorio de Farmacognosia y Productos Naturales, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Guillermo Moyna
- Laboratorio de Fisicoquímica Orgánica, Departamento de Química del Litoral, Centro Universitario Regional Litoral Norte, Universidad de la República, Paysandú, Uruguay
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Danzi F, Pacchiana R, Mafficini A, Scupoli MT, Scarpa A, Donadelli M, Fiore A. To metabolomics and beyond: a technological portfolio to investigate cancer metabolism. Signal Transduct Target Ther 2023; 8:137. [PMID: 36949046 PMCID: PMC10033890 DOI: 10.1038/s41392-023-01380-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.
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Affiliation(s)
- Federica Danzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria T Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, Biology and Genetics Section, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
| | - Alessandra Fiore
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
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Wang H, Falcoz S, Morales J, Berteau JP. Investigating bone resorption in Atlantic herring fish intermuscular bones with solid-state NMR. Phys Chem Chem Phys 2023; 25:9336-9348. [PMID: 36920434 DOI: 10.1039/d2cp03023c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Bones are connective tissues mainly made of collagen proteins with calcium phosphate deposits. They undergo constant remodeling, including destroying existing bones tissues (known as bone resorption) and rebuilding new ones. Bone remodeling has been well-described in mammals, but it is not the case in fish. Here, we focused on the mobile phase of the bone vascular system by carefully preserving moisture in adult Atlantic herring intermuscular bones. We detected pore water with high ionic strength and soluble degraded peptides whose 1H-transverse relaxation times, T2s, exceed 15 milliseconds. With favorable T2s, we incorporated a solution state spinlock scheme into the INEPT techniques to unequivocally demonstrate collagen degradation. In addition, we detected a substantial amount of inorganic phosphate in solution with 31P-NMR in the considerable background of solid hydroxyapatite calcium phosphate by saturation recovery experiment. It is consistent with the idea that bone resorption degrades bone collagen and releases calcium ions and phosphate ions in the pore water with increased ionic strength. Our report is the first to probe the resorption process in the heterogenous bone microstructure with a rigorous characterization of 1H and 13C relaxation behavior and direct assignments. In addition, we contribute to the fish bones literature by investigating fish bone remodeling using NMR for the first time.
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Affiliation(s)
- Hsin Wang
- Department of Chemistry and Biochemistry, The City College of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA.
| | - Steve Falcoz
- Department of Physical Therapy, The College of Staten Island, 2800 Victory Blvd, Staten Island, NY 10314, USA
| | - Jorge Morales
- Department of Chemistry and Biochemistry, The City College of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA.
| | - Jean-Philippe Berteau
- Department of Physical Therapy, The College of Staten Island, 2800 Victory Blvd, Staten Island, NY 10314, USA.,New York Centre for Biomedical Engineering, City University of New York - City College of New York, New York 10031, USA.,Nanosciences Initiative, City University of New York - Advanced Science Research Center, New York 10031, USA
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65
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Benjamin DI, Brett JO, Both P, Benjamin JS, Ishak HL, Kang J, Kim S, Chung M, Arjona M, Nutter CW, Tan JH, Krishnan AK, Dulay H, Louie SM, de Morree A, Nomura DK, Rando TA. Multiomics reveals glutathione metabolism as a driver of bimodality during stem cell aging. Cell Metab 2023; 35:472-486.e6. [PMID: 36854304 PMCID: PMC10015599 DOI: 10.1016/j.cmet.2023.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/14/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
With age, skeletal muscle stem cells (MuSCs) activate out of quiescence more slowly and with increased death, leading to defective muscle repair. To explore the molecular underpinnings of these defects, we combined multiomics, single-cell measurements, and functional testing of MuSCs from young and old mice. The multiomics approach allowed us to assess which changes are causal, which are compensatory, and which are simply correlative. We identified glutathione (GSH) metabolism as perturbed in old MuSCs, with both causal and compensatory components. Contrary to young MuSCs, old MuSCs exhibit a population dichotomy composed of GSHhigh cells (comparable with young MuSCs) and GSHlow cells with impaired functionality. Mechanistically, we show that antagonism between NRF2 and NF-κB maintains this bimodality. Experimental manipulation of GSH levels altered the functional dichotomy of aged MuSCs. These findings identify a novel mechanism of stem cell aging and highlight glutathione metabolism as an accessible target for reversing MuSC aging.
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Affiliation(s)
- Daniel I Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jamie O Brett
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Pieter Both
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Joel S Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Heather L Ishak
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingyu Chung
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina Arjona
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Nutter
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jenna H Tan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Ananya K Krishnan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Hunter Dulay
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon M Louie
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Neurology Service, Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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66
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Liu W, Zhang L, Bao L, Shen G, Feng J. Accurate Classification and Prediction of Acute Myocardial Infarction through an ARMD Procedure. J Proteome Res 2023; 22:758-767. [PMID: 36710647 DOI: 10.1021/acs.jproteome.2c00488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The risk stratification of acute myocardial infarction (AMI) patients is of prime importance for clinical management and prognosis assessment. Thus, we propose an ensemble machine learning analysis procedure named ADASYN-RFECV-MDA-DNN (ARMD) to address sample-unbalanced problems and enable stratification and prediction of AMI outcomes. The ARMD analysis procedure was applied to the NMR data of sera from 534 AMI-related subjects in four categories with an extremely imbalanced sample proportion. Firstly, the adaptive synthetic sampling (ADASYN) algorithm was used to address the issue of the original sample imbalance. Secondly, the recursive feature elimination with cross-validation (RFECV) processing and random forest mean decrease accuracy (RF-MDA) algorithm was performed to identify the differential metabolites corresponding to each AMI outcome. Finally, the deep neural network (DNN) was employed to classify and predict AMI events, and its performance was evaluated by comparing the four traditional machine learning methods. Compared with the other four machine learning models, DNN presented consistent superiority in almost all of the model parameters including precision, f1-score, sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and classification accuracy, highlighting the potential of deep learning in classification and stratification of clinical diseases. The ARMD analysis procedure was a practical analysis tool for supervised classification and regression modeling of clinical diseases.
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Affiliation(s)
- Wuping Liu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Siming District, Xiamen, Fujian 361005, China
| | - Lirong Zhang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Siming District, Xiamen, Fujian 361005, China
| | - Lijun Bao
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Siming District, Xiamen, Fujian 361005, China
| | - Guiping Shen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Siming District, Xiamen, Fujian 361005, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, 422 Siming South Road, Siming District, Xiamen, Fujian 361005, China
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67
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Kwan B, Fuhrer T, Montemayor D, Fink JC, He J, Hsu CY, Messer K, Nelson RG, Pu M, Ricardo AC, Rincon-Choles H, Shah VO, Ye H, Zhang J, Sharma K, Natarajan L. A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study. BMC Bioinformatics 2023; 24:57. [PMID: 36803209 PMCID: PMC9942303 DOI: 10.1186/s12859-023-05171-w] [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] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND The growing amount of high dimensional biomolecular data has spawned new statistical and computational models for risk prediction and disease classification. Yet, many of these methods do not yield biologically interpretable models, despite offering high classification accuracy. An exception, the top-scoring pair (TSP) algorithm derives parameter-free, biologically interpretable single pair decision rules that are accurate and robust in disease classification. However, standard TSP methods do not accommodate covariates that could heavily influence feature selection for the top-scoring pair. Herein, we propose a covariate-adjusted TSP method, which uses residuals from a regression of features on the covariates for identifying top scoring pairs. We conduct simulations and a data application to investigate our method, and compare it to existing classifiers, LASSO and random forests. RESULTS Our simulations found that features that were highly correlated with clinical variables had high likelihood of being selected as top scoring pairs in the standard TSP setting. However, through residualization, our covariate-adjusted TSP was able to identify new top scoring pairs, that were largely uncorrelated with clinical variables. In the data application, using patients with diabetes (n = 977) selected for metabolomic profiling in the Chronic Renal Insufficiency Cohort (CRIC) study, the standard TSP algorithm identified (valine-betaine, dimethyl-arg) as the top-scoring metabolite pair for classifying diabetic kidney disease (DKD) severity, whereas the covariate-adjusted TSP method identified the pair (pipazethate, octaethylene glycol) as top-scoring. Valine-betaine and dimethyl-arg had, respectively, ≥ 0.4 absolute correlation with urine albumin and serum creatinine, known prognosticators of DKD. Thus without covariate-adjustment the top-scoring pair largely reflected known markers of disease severity, whereas covariate-adjusted TSP uncovered features liberated from confounding, and identified independent prognostic markers of DKD severity. Furthermore, TSP-based methods achieved competitive classification accuracy in DKD to LASSO and random forests, while providing more parsimonious models. CONCLUSIONS We extended TSP-based methods to account for covariates, via a simple, easy to implement residualizing process. Our covariate-adjusted TSP method identified metabolite features, uncorrelated from clinical covariates, that discriminate DKD severity stage based on the relative ordering between two features, and thus provide insights into future studies on the order reversals in early vs advanced disease states.
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Grants
- R01 DK110541 NIDDK NIH HHS
- U24 DK060990 NIDDK NIH HHS
- R01DK118736, 1R01DK110541-01A1, U01DK060990, U01DK060984, U01DK061022, U01DK061021, U01DK061028, U01DK060980, U01DK060963, U01DK060902, U24DK060990 NIDDK NIH HHS
- National Science Foundation Graduate Research Fellowship Program
- Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases
- National Institute of Diabetes and Digestive and Kidney Diseases
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Affiliation(s)
- Brian Kwan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Montemayor
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jeffery C Fink
- Department of Medicine, University of Maryland, Baltimore School of Medicine, Baltimore, MD, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine and Tulane University Translational Science Institute,, New Orleans, LA, USA
| | - Chi-Yuan Hsu
- Division of Nephrology, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Karen Messer
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Minya Pu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Ana C Ricardo
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Hernan Rincon-Choles
- Department of Nephrology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Vallabh O Shah
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Hongping Ye
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Kumar Sharma
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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Plasma Metabolite Signatures in Male Carriers of Genetic Variants Associated with Non-Alcoholic Fatty Liver Disease. Metabolites 2023; 13:metabo13020267. [PMID: 36837886 PMCID: PMC9964056 DOI: 10.3390/metabo13020267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/01/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Both genetic and non-genetic factors are important in the pathophysiology of non-alcoholic fatty liver disease (NAFLD). The aim of our study was to identify novel metabolites and pathways associated with NAFLD by including both genetic and non-genetic factors in statistical analyses. We genotyped six genetic variants in the PNPLA3, TM6SF2, MBOAT7, GCKR, PPP1R3B, and HSD17B13 genes reported to be associated with NAFLD. Non-targeted metabolomic profiling was performed from plasma samples. We applied a previously validated fatty liver index to identify participants with NAFLD. First, we associated the six genetic variants with 1098 metabolites in 2 339 men without NAFLD to determine the effects of the genetic variants on metabolites, and then in 2 535 men with NAFLD to determine the joint effects of genetic variants and non-genetic factors on metabolites. We identified several novel metabolites and metabolic pathways, especially for PNPLA3, GCKR, and PPP1R38 variants relevant to the pathophysiology of NAFLD. Importantly, we showed that each genetic variant for NAFLD had a specific metabolite signature. The plasma metabolite signature was unique for each genetic variant, suggesting that several metabolites and different pathways are involved in the risk of NAFLD. The FLI index reliably identifies metabolites for NAFLD in large population-based studies.
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Elevated 18:0 lysophosphatidylcholine contributes to the development of pain in tissue injury. Pain 2023; 164:e103-e115. [PMID: 36638307 PMCID: PMC9833116 DOI: 10.1097/j.pain.0000000000002709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 02/06/2023]
Abstract
ABSTRACT Tissue injuries, including burns, are major causes of death and morbidity worldwide. These injuries result in the release of intracellular molecules and subsequent inflammatory reactions, changing the tissues' chemical milieu and leading to the development of persistent pain through activating pain-sensing primary sensory neurons. However, the majority of pain-inducing agents in injured tissues are unknown. Here, we report that, amongst other important metabolite changes, lysophosphatidylcholines (LPCs) including 18:0 LPC exhibit significant and consistent local burn injury-induced changes in concentration. 18:0 LPC induces immediate pain and the development of hypersensitivities to mechanical and heat stimuli through molecules including the transient receptor potential ion channel, vanilloid subfamily, member 1, and member 2 at least partly via increasing lateral pressure in the membrane. As levels of LPCs including 18:0 LPC increase in other tissue injuries, our data reveal a novel role for these lipids in injury-associated pain. These findings have high potential to improve patient care.
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Song Y, Song Q, Liu W, Li J, Tu P. High-confidence structural identification of metabolites relying on tandem mass spectrometry through isomeric identification: A tutorial. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Tian Y, Li G, Du X, Zeng T, Chen L, Xu W, Gu T, Tao Z, Lu L. Integration of LC-MS-Based and GC-MS-Based Metabolic Profiling to Reveal the Effects of Domestication and Boiling on the Composition of Duck Egg Yolks. Metabolites 2023; 13:metabo13010135. [PMID: 36677059 PMCID: PMC9866831 DOI: 10.3390/metabo13010135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Egg yolks contain abundant lipids, proteins, and minerals that provide not only essential nutrients for embryonic development but also cheap sources of nutrients for consumers worldwide. Previous composition analyses of egg yolks primarily focused on nutrients such as lipids and minerals. However, few studies have reported the effects of domestication and heating on yolk composition and characteristics. The objective of this study was to investigate the impact of domestication and boiling on the metabolite contents of egg yolks via untargeted metabolomics using GC-MS and LC-MS. In this study, eggs were collected from Fenghua teals, captive mallards, and Shaoxing ducks. Twelve duck eggs (half raw and half cooked) were randomly selected from each variety, and the egg yolks were separated for metabolic profiling. The analysis identified 1205 compounds in the egg yolks. Domestication generated more differential metabolites than boiling, which indicated that the changes in the metabolome of duck egg yolk caused by domestication were greater than those caused by boiling. In a comparative analysis of domestic and mallard ducks, 48 overlapping differential metabolites were discovered. Among them, nine metabolites were upregulated in domesticated ducks, including monoolein, emodin, daidzein, genistein, and glycitein, which may be involved in lipid metabolism; some of them may also act as phytoestrogens (flavonoids). Another 39 metabolites, including imethylethanolamine, harmalan, mannitol, nornicotine, linoleic acid, diphenylamine, proline betaine, alloxanthin, and resolvin d1, were downregulated by domestication and were linked to immunity, anti-inflammatory, antibacterial, and antioxidant properties. Furthermore, four overlapping differential metabolites that included amino acids and dipeptides were discovered in paired comparisons of the raw and boiled samples. Our findings provided new insights into the molecular response of duck domestication and supported the use of metabolomics to examine the impact of boiling on the composition of egg yolks.
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Affiliation(s)
- Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
| | - Guoqin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
| | - Xizhong Du
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua 321017, China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
| | - Tiantian Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
| | - Zhengrong Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310021, China
- Correspondence: ; Tel.: +86-571-8640-6682
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Yu Z, Wang L, Wu S, Zhao W. Dissecting the potential mechanism of antihypertensive effects of RVPSL on spontaneously hypertensive rats via widely targeted kidney metabolomics. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:428-436. [PMID: 36373790 DOI: 10.1002/jsfa.12157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Our previous study has demonstrated that the egg-white-derived peptide RVPSL can lower blood pressure in spontaneously hypertensive rats (SHRs), but its potential action mechanism remains unclear. In this work, the underlying mechanism of the antihypertensive effects of RVPSL in SHRs was elucidated using the widely targeted kidney metabolomics approach. RESULTS Ten SHRs were divided into two groups: SHR-Untreated group (0.9% saline) and SHR-RVPSL group (50 mg kg-1 body weight RVPSL) for 4 weeks. After 4 weeks, kidney samples were collected and widely targeted (liquid chromatography-electrospray ionization-tandem mass spectrometry) metabolomics was used to detect metabolites. Fifty-six biomarkers were identified that may be associated with hypertension. Among them, 17 biomarkers were upregulated and 39 biomarkers were downregulated. The results suggested that eight potential biomarkers were identified in kidney samples: O-phospho-l-serine, tyramine, citric acid, 3-hydroxybutyrate, O-acetyl-l-serine, 15-oxo-5Z,8Z,11Z,13E-eicosatetraenoic acid (15-oxoETE), dopaquinone and 3,3',5-triiodo-l-thyronine. These potential biomarkers mainly involved carbon metabolism, thyroid hormone signaling pathway, tyrosine metabolism and arachidonic acid metabolism. CONCLUSION The study suggested that RVPSL may exert antihypertensive effects through upregulation of O-phospho-l-serine, 3-hydroxybutyrate and 15-oxoETE, and downregulation of tyramine, citric acid, O-acetyl-l-serine, 3,3',5-triiodo-l-thyronine and dopaquinone. The antihypertensive effects of RVPSL may be related to carbon metabolism, thyroid hormone signaling pathway, tyrosine metabolism and arachidonic acid metabolism. RVPSL exhibited a potent antihypertensive effect, and the antihypertensive effects were associated with inhibition of vascular smooth muscle cell proliferation, vascular remodeling, vascular endothelium dysfunction, restoring reactive oxygen species, oxidative stress, inflammation and immune reaction. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhipeng Yu
- School of Food Science and Engineering, Hainan University, Haikou, PR China
| | - Li Wang
- College of Food Science and Engineering, Bohai University, Jinzhou, PR China
| | - Sijia Wu
- Laboratory of Nutrition and Functional Food, Jilin University, Changchun, PR China
| | - Wenzhu Zhao
- School of Food Science and Engineering, Hainan University, Haikou, PR China
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Unsupervised Analysis of Small Molecule Mixtures by Wavelet-Based Super-Resolved NMR. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020792. [PMID: 36677850 PMCID: PMC9866129 DOI: 10.3390/molecules28020792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023]
Abstract
Resolving small molecule mixtures by nuclear magnetic resonance (NMR) spectroscopy has been of great interest for a long time for its precision, reproducibility, and efficiency. However, spectral analyses for such mixtures are often highly challenging due to overlapping resonance lines and limited chemical shift windows. The existing experimental and theoretical methods to produce shift NMR spectra in dealing with the problem have limited applicability owing to sensitivity issues, inconsistency, and/or the requirement of prior knowledge. Recently, we resolved the problem by decoupling multiplet structures in NMR spectra by the wavelet packet transform (WPT) technique. In this work, we developed a scheme for deploying the method in generating highly resolved WPT NMR spectra and predicting the composition of the corresponding molecular mixtures from their 1H NMR spectra in an automated fashion. The four-step spectral analysis scheme consists of calculating the WPT spectrum, peak matching with a WPT shift NMR library, followed by two optimization steps in producing the predicted molecular composition of a mixture. The robustness of the method was tested on an augmented dataset of 1000 molecular mixtures, each containing 3 to 7 molecules. The method successfully predicted the constituent molecules with a median true positive rate of 1.0 against the varying compositions, while a median false positive rate of 0.04 was obtained. The approach can be scaled easily for much larger datasets.
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Zebiri I, Jacquette B, Francezon N, Herbaut M, Latigui A, Bricaud S, Tremblay R, Pasetto P, Mouget JL, Dittmer J. The Polysaccharidic Nature of the Skeleton of Marennine as Determined by NMR Spectroscopy. Mar Drugs 2023; 21:md21010042. [PMID: 36662215 PMCID: PMC9865362 DOI: 10.3390/md21010042] [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: 11/27/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
The water-soluble blue-green pigment marennine, produced and partly excreted by the diatom Haslea ostrearia, and known for a long time for its role in the greening of oysters, was isolated from the culture medium, purified, and analyzed by Nuclear Magnetic Resonance (NMR) in order to gain insight into its chemical structure. The spectra show mainly carbohydrates of a complex composition, apparently highly branched, and with a mass in the order of 10 kDa. There are, in addition, some signals of aliphatic and, much weaker, aromatic groups that present aglycons. The latter might be responsible for the color. These carbohydrates are always associated with the blue-green color and cannot be separated from it by most treatments; they are interpreted as constituting the frame of the pigment. NMR after hydrolysis identifies the most abundant monosaccharides in marennine as galactose, xylose, mannose, rhamnose, and fucose.
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Affiliation(s)
- Ilhem Zebiri
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Boris Jacquette
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Nellie Francezon
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Mickaël Herbaut
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Amina Latigui
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Sullivan Bricaud
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Réjean Tremblay
- Institut des Sciences de la Mer, Université du Québec à Rimouski, 310 Allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Pamela Pasetto
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Jean-Luc Mouget
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
| | - Jens Dittmer
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Le Mans Université, Av. Olivier Messiaen, 72085 Le Mans, France
- Correspondence: (J.D.)
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Karlsen E, Gylseth M, Schulz C, Almaas E. A study of a diauxic growth experiment using an expanded dynamic flux balance framework. PLoS One 2023; 18:e0280077. [PMID: 36607958 PMCID: PMC9821518 DOI: 10.1371/journal.pone.0280077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Flux balance analysis (FBA) remains one of the most used methods for modeling the entirety of cellular metabolism, and a range of applications and extensions based on the FBA framework have been generated. Dynamic flux balance analysis (dFBA), the expansion of FBA into the time domain, still has issues regarding accessibility limiting its widespread adoption and application, such as a lack of a consistently rigid formalism and tools that can be applied without expert knowledge. Recent work has combined dFBA with enzyme-constrained flux balance analysis (decFBA), which has been shown to greatly improve accuracy in the comparison of computational simulations and experimental data, but such approaches generally do not take into account the fact that altering the enzyme composition of a cell is not an instantaneous process. Here, we have developed a decFBA method that explicitly takes enzyme change constraints (ecc) into account, decFBAecc. The resulting software is a simple yet flexible framework for using genome-scale metabolic modeling for simulations in the time domain that has full interoperability with the COBRA Toolbox 3.0. To assess the quality of the computational predictions of decFBAecc, we conducted a diauxic growth fermentation experiment with Escherichia coli BW25113 in glucose minimal M9 medium. The comparison of experimental data with dFBA, decFBA and decFBAecc predictions demonstrates how systematic analyses within a fixed constraint-based framework can aid the study of model parameters. Finally, in explaining experimentally observed phenotypes, our computational analysis demonstrates the importance of non-linear dependence of exchange fluxes on medium metabolite concentrations and the non-instantaneous change in enzyme composition, effects of which have not previously been accounted for in constraint-based analysis.
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Affiliation(s)
- Emil Karlsen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Marianne Gylseth
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Christian Schulz
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K. G. Jebsen Center for Genetic Epidemiology Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
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Xia F, Wan JB. Chemical derivatization strategy for mass spectrometry-based lipidomics. MASS SPECTROMETRY REVIEWS 2023; 42:432-452. [PMID: 34486155 DOI: 10.1002/mas.21729] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/02/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Lipids, serving as the structural components of cellular membranes, energy storage, and signaling molecules, play the essential and multiple roles in biological functions of mammals. Mass spectrometry (MS) is widely accepted as the first choice for lipid analysis, offering good performance in sensitivity, accuracy, and structural characterization. However, the untargeted qualitative profiling and absolute quantitation of lipids are still challenged by great structural diversity and high structural similarity. In recent decade, chemical derivatization mainly targeting carboxyl group and carbon-carbon double bond of lipids have been developed for lipidomic analysis with diverse advantages: (i) offering more characteristic structural information; (ii) improving the analytical performance, including chromatographic separation and MS sensitivity; (iii) providing one-to-one chemical isotope labeling internal standards based on the isotope derivatization regent in quantitative analysis. Moreover, the chemical derivatization strategy has shown great potential in combination with ion mobility mass spectrometry and ambient mass spectrometry. Herein, we summarized the current states and advances in chemical derivatization-assisted MS techniques for lipidomic analysis, and their strengths and challenges are also given. In summary, the chemical derivatization-based lipidomic approach has become a promising and reliable technique for the analysis of lipidome in complex biological samples.
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Affiliation(s)
- Fangbo Xia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Jian-Bo Wan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
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Treeriya R, Ho PN, Titapun A, Klanrit P, Suksawat M, Kulthawatsiri T, Sirirattanakul S, Loilome W, Namwat N, Wangwiwatsin A, Chamadol N, Khuntikeo N, Phetcharaburanin J. 1H NMR fecal metabolic phenotyping of periductal fibrosis- and cholangiocarcinoma-specific metabotypes defining perturbation in gut microbial-host co-metabolism. PeerJ 2023; 11:e15386. [PMID: 37187520 PMCID: PMC10178365 DOI: 10.7717/peerj.15386] [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: 10/12/2022] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Background The liver fluke Opisthorchis viverrini (OV), which subsequently inhabits the biliary system and results in periductal fibrosis (PDF), is one of the primarily causes of cholangiocarcinoma (CCA), a bile duct cancer with an exceptionally high incidence in the northeast of Thailand and other Greater Mekong Subregion (GMS) countries. Insights in fecal metabolic changes associated with PDF and CCA are required for further molecular research related to gut health and potential diagnostic biological marker development. Methods In this study, nuclear magnetic resonance (NMR) metabolomics was applied for fecal metabolic phenotyping from 55 fecal water samples across different study groups including normal bile duct, PDF and CCA groups. Results By using NMR spectroscopy-based metabolomics, fecal metabolic profiles of patients with CCA or PDF and of individuals with normal bile duct have been established with a total of 40 identified metabolites. Further multivariate statistical analysis and hierarchical clustering heat map have demonstrated the PDF- and CCA-specific metabotypes through various altered metabolite groups including amino acids, alcohols, amines, anaerobic glycolytic metabolites, fatty acids, microbial metabolites, sugar, TCA cycle intermediates, tryptophan catabolism substrates, and pyrimidine metabolites. Compared to the normal bile duct group, PDF individuals showed the significantly elevated relative concentrations of fecal ethanol, glycine, tyrosine, and N-acetylglucosamine whereas CCA patients exhibited the remarkable fecal metabolic changes that can be evident through the increased relative concentrations of fecal uracil, succinate, and 5-aminopentanoate. The prominent fecal metabolic alterations between CCA and PDF were displayed by the reduction of relative concentration of methanol observed in CCA. The metabolic alterations associated with PDF and CCA progression have been proposed with the involvement of various metabolic pathways including TCA cycle, ethanol biogenesis, hexamine pathway, methanol biogenesis, pyrimidine metabolism, and lysine metabolism. Among them, ethanol, methanol, and lysine metabolism strongly reflect the association of gut-microbial host metabolic crosstalk in PDF and/or CCA patients. Conclusion The PDF- and CCA-associated metabotypes have been investigated displaying their distinct fecal metabolic patterns compared to that of normal bile duct group. Our study also demonstrated that the perturbation in co-metabolism of host and gut bacteria has been involved from the early step since OV infection to CCA tumorigenesis.
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Affiliation(s)
- Rujikorn Treeriya
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Phuc N. Ho
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Attapol Titapun
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Poramate Klanrit
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Manida Suksawat
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanaporn Kulthawatsiri
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Suphasarang Sirirattanakul
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Watcharin Loilome
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nisana Namwat
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Arporn Wangwiwatsin
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nittaya Chamadol
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Jutarop Phetcharaburanin
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
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Ahmad F, Nadeem H. Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery. Methods Mol Biol 2023; 2575:77-103. [PMID: 36301472 DOI: 10.1007/978-1-0716-2716-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.
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Affiliation(s)
- Faheem Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Hera Nadeem
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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79
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Braisted J, Patt A, Tindall C, Sheils T, Neyra J, Spencer K, Eicher T, Mathé EA. RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes. Bioinformatics 2023; 39:6827287. [PMID: 36373969 PMCID: PMC9825745 DOI: 10.1093/bioinformatics/btac726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/19/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
MOTIVATION Functional interpretation of high-throughput metabolomic and transcriptomic results is a crucial step in generating insight from experimental data. However, pathway and functional information for genes and metabolites are distributed among many siloed resources, limiting the scope of analyses that rely on a single knowledge source. RESULTS RaMP-DB 2.0 is a web interface, relational database, API and R package designed for straightforward and comprehensive functional interpretation of metabolomic and multi-omic data. RaMP-DB 2.0 has been upgraded with an expanded breadth and depth of functional and chemical annotations (ClassyFire, LIPID MAPS, SMILES, InChIs, etc.), with new data types related to metabolites and lipids incorporated. To streamline entity resolution across multiple source databases, we have implemented a new semi-automated process, thereby lessening the burden of harmonization and supporting more frequent updates. The associated RaMP-DB 2.0 R package now supports queries on pathways, common reactions (e.g. metabolite-enzyme relationship), chemical functional ontologies, chemical classes and chemical structures, as well as enrichment analyses on pathways (multi-omic) and chemical classes. Lastly, the RaMP-DB web interface has been completely redesigned using the Angular framework. AVAILABILITY AND IMPLEMENTATION The code used to build all components of RaMP-DB 2.0 are freely available on GitHub at https://github.com/ncats/ramp-db, https://github.com/ncats/RaMP-Client/ and https://github.com/ncats/RaMP-Backend. The RaMP-DB web application can be accessed at https://rampdb.nih.gov/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Cole Tindall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | - Timothy Sheils
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | | | - Kyle Spencer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Tara Eicher
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
- Department of Computer Science and Engineering, The Ohio State University, Columbus OH 43210, USA
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80
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Arya N, Marincin KA, Frueh DP. Probing Substrate-Loaded Carrier Proteins by Nuclear Magnetic Resonance. Methods Mol Biol 2023; 2670:235-253. [PMID: 37184708 DOI: 10.1007/978-1-0716-3214-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Carrier proteins (CPs) are central actors in nonribosomal peptide synthetases (NRPSs) as they interact with all catalytic domains, and because they covalently hold the substrates and intermediates leading to the final product. Thus, how CPs and their partner domains recognize and engage with each other as a function of CP cargos is paramount to understanding and engineering NRPSs. However, rapid hydrolysis of the labile thioester bonds holding substrates challenges molecular and biophysical studies to determine the molecular mechanisms of domain recognition. In this chapter, we describe a protocol to counteract hydrolysis and study loaded carrier proteins at the atomic level with nuclear magnetic resonance (NMR) spectroscopy. The method relies on loading CPs in situ, with adenylation domains in the NMR tube, to reach substrate-loaded CPs at steady state. We describe controls and experimental readouts necessary to assess the integrity of the sample and maintain loading on CPs. Our approach provides a basis to conduct subsequent NMR experiments and obtain kinetic, thermodynamic, dynamic, and structural parameters of substrate-loaded CPs alone or in the presence of other domains.
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Affiliation(s)
- Neeru Arya
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth A Marincin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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81
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Abstract
Metabolomics has long been used in a biomedical context. The most typical samples are body fluids in which small molecules can be detected and quantified using technologies such as Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). Many studies, in particular in the wider field of cancer research, are based on cellular models. Different cancer cells can have vastly different ways of regulating metabolism and responses to drug treatments depend on specific metabolic mechanisms which are often cell type specific. This has led to a series of publications using metabolomics to study metabolic mechanisms. Cell-based metabolomics has specific requirements and allows for interesting approaches where metabolism is followed in real-time. Here applications of metabolomics in cell biology have been reviewed, providing insight into specific technologies used and showing exemplary case studies with an emphasis towards applications which help to understand drug mechanisms.
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Affiliation(s)
- Zuhal Eraslan
- Department of Dermatology, Weill Cornell Medicine, New York, NY, USA
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona, Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Ulrich L Günther
- Institute of Chemistry and Metabolomics, University of Lübeck, Lübeck, Germany.
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82
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Bouranis JA, Beaver LM, Jiang D, Choi J, Wong CP, Davis EW, Williams DE, Sharpton TJ, Stevens JF, Ho E. Interplay between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach. Nutrients 2022; 15:nu15010042. [PMID: 36615700 PMCID: PMC9824405 DOI: 10.3390/nu15010042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Brassica vegetables contain a multitude of bioactive compounds that prevent and suppress cancer and promote health. Evidence suggests that the gut microbiome may be essential in the production of these compounds; however, the relationship between specific microbes and the abundance of metabolites produced during cruciferous vegetable digestion are still unclear. We utilized an ex vivo human fecal incubation model with in vitro digested broccoli sprouts (Broc), Brussels sprouts (Brus), a combination of the two vegetables (Combo), or a negative control (NC) to investigate microbial metabolites of cruciferous vegetables. We conducted untargeted metabolomics on the fecal cultures by LC-MS/MS and completed 16S rRNA gene sequencing. We identified 72 microbial genera in our samples, 29 of which were significantly differentially abundant between treatment groups. A total of 4499 metabolomic features were found to be significantly different between treatment groups (q ≤ 0.05, fold change > 2). Chemical enrichment analysis revealed 45 classes of compounds to be significantly enriched by brassicas, including long-chain fatty acids, coumaric acids, and peptides. Multi-block PLS-DA and a filtering method were used to identify microbe−metabolite interactions. We identified 373 metabolites from brassica, which had strong relationships with microbes, such as members of the family Clostridiaceae and genus Intestinibacter, that may be microbially derived.
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Affiliation(s)
- John A. Bouranis
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Laura M. Beaver
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
| | - Jaewoo Choi
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Carmen P. Wong
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Edward W. Davis
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - David E. Williams
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Thomas J. Sharpton
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Jan F. Stevens
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Emily Ho
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
- Correspondence:
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83
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Hatmaker EA, Rangel-Grimaldo M, Raja HA, Pourhadi H, Knowles SL, Fuller K, Adams EM, Lightfoot JD, Bastos RW, Goldman GH, Oberlies NH, Rokas A. Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives. Microbiol Spectr 2022; 10:e0306922. [PMID: 36318036 PMCID: PMC9769809 DOI: 10.1128/spectrum.03069-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal diseases affect millions of humans annually, yet fungal pathogens remain understudied. The mold Aspergillus flavus can cause both aspergillosis and fungal keratitis infections, but closely related species are not considered clinically relevant. To study the evolution of A. flavus pathogenicity, we examined genomic and phenotypic traits of two strains of A. flavus and three closely related species, Aspergillus arachidicola (two strains), Aspergillus parasiticus (two strains), and Aspergillus nomiae (one strain). We identified >3,000 orthologous proteins unique to A. flavus, including seven biosynthetic gene clusters present in A. flavus strains and absent in the three nonpathogens. We characterized secondary metabolite production for all seven strains under two clinically relevant conditions, temperature and salt concentration. Temperature impacted metabolite production in all species, whereas salinity did not affect production of any species. Strains of the same species produced different metabolites. Growth under stress conditions revealed additional heterogeneity within species. Using the invertebrate fungal disease model Galleria mellonella, we found virulence of strains of the same species varied widely; A. flavus strains were not more virulent than strains of the nonpathogens. In a murine model of fungal keratitis, we observed significantly lower disease severity and corneal thickness for A. arachidicola compared to other species at 48 h postinfection, but not at 72 h. Our work identifies variations in key phenotypic, chemical, and genomic attributes between A. flavus and its nonpathogenic relatives and reveals extensive strain heterogeneity in virulence that does not correspond to the currently established clinical relevance of these species. IMPORTANCE Aspergillus flavus is a filamentous fungus that causes opportunistic human infections, such as aspergillosis and fungal keratitis, but its close relatives are considered nonpathogenic. To begin understanding how this difference in pathogenicity evolved, we characterized variation in infection-relevant genomic, chemical, and phenotypic traits between strains of A. flavus and its relatives. We found extensive variation (or strain heterogeneity) within the pathogenic A. flavus as well as within its close relatives, suggesting that strain-level differences may play a major role in the ability of these fungi to cause disease. Surprisingly, we also found that the virulence of strains from species not considered to be pathogens was similar to that of A. flavus in both invertebrate and murine models of disease. These results contrast with previous studies on Aspergillus fumigatus, another major pathogen in the genus, for which significant differences in infection-relevant chemical and phenotypic traits are observed between closely related pathogenic and nonpathogenic species.
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Affiliation(s)
- E. Anne Hatmaker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Manuel Rangel-Grimaldo
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Huzefa A. Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Hadi Pourhadi
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Sonja L. Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Kevin Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Emily M. Adams
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Jorge D. Lightfoot
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Rafael W. Bastos
- Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Nicholas H. Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
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84
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Sinha Roy A, Srivastava M. Analysis of Small-Molecule Mixtures by Super-Resolved 1H NMR Spectroscopy. J Phys Chem A 2022; 126:9108-9113. [PMID: 36413171 DOI: 10.1021/acs.jpca.2c06858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Analysis of small molecules is essential to metabolomics, natural products, drug discovery, food technology, and many other areas of interest. Current barriers preclude from identifying the constituent molecules in a mixture as overlapping clusters of NMR lines pose a major challenge in resolving signature frequencies for individual molecules. While homonuclear decoupling techniques produce much simplified pure shift spectra, they often affect sensitivity. Conversion of typical NMR spectra to pure shift spectra by signal processing without a priori knowledge about the coupling patterns is essential for accurate analysis. We developed a super-resolved wavelet packet transform based 1H NMR spectroscopy that can be used in high-throughput studies to reliably decouple individual constituents of small molecule mixtures. We demonstrate the efficacy of the method on the model mixtures of saccharides and amino acids in the presence of significant noise.
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Affiliation(s)
- Aritro Sinha Roy
- Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-0001,United States
| | - Madhur Srivastava
- Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-0001,United States.,National Biomedical Resources for Advanced ESR Technologies (ACERT), Ithaca, New York 14853, United States
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85
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Koopman J, Grimme S. Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2226-2242. [PMID: 36343304 DOI: 10.1021/jasms.2c00209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.
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Affiliation(s)
- Jeroen Koopman
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115Bonn, Germany
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86
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Melvin SD, Chaousis S, Finlayson K, Carroll AR, van de Merwe JP. Field-scale monitoring of green sea turtles (Chelonia mydas): Influence of site characteristics and capture technique on the blood metabolome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101026. [PMID: 36191476 DOI: 10.1016/j.cbd.2022.101026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 01/27/2023]
Abstract
Given their threatened status, there is considerable interest in establishing monitoring techniques that can be used to evaluate the health of sea turtles in the wild. The present study represents a methodological contribution towards field-scale metabolomic assessment of sea turtles, by exploring differences in blood biochemistry associated with site characteristics and capture technique. We compared the metabolome of blood from animals at three locations (two coastal and one reefal), collected from turtles that were either resting or active, and sampled across multiple seasons at one location. Our results show clear differences in the metabolome of turtles from the three locations, some of which are likely attributable to differences in diet or forage quality and others which may reflect differences in other factors (e.g., occurrence of land-based contaminants or other biotic and/or abiotic stressors) between coastal and reefal sites. Our analysis also revealed the influence of capture technique on metabolite profiles, with numerous markers of physical exertion in animals captured while active that were absent in turtles sampled while resting. We observed a modest potential for temporal differences in the metabolome, but controlling for sampling time did not change the overall conclusions of our study. This suggests that temporal differences in the metabolome warrant consideration when designing studies to evaluate the status of sea turtles in the wild, but that site characteristics and capture technique are bigger drivers. However, sample size for this comparison was relatively small and further investigation of seasonal differences in the metabolome are warranted. Research exploring each of these factors more closely will further contribute towards achieving robust metabolomics analysis of sea turtles across large spatial and temporal scales.
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Affiliation(s)
- Steven D Melvin
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia.
| | - Stephanie Chaousis
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia
| | - Kimberly Finlayson
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia
| | - Anthony R Carroll
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Southport, QLD, Australia
| | - Jason P van de Merwe
- Australian Rivers Institute, School of Environment and Science, Griffith University, Southport, Queensland, Australia. https://twitter.com/@DrVanders
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87
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Sol J, Colàs-Campàs L, Mauri-Capdevila G, Molina-Seguin J, Galo-Licona JD, Torres-Querol C, Aymerich N, Ois Á, Roquer J, Tur S, García-Carreira MDC, Martí-Fàbregas J, Cruz-Culebras A, Segura T, Pamplona R, Portero-Otín M, Arqué G, Jové M, Purroy F. Ischemia preconditioning induces an adaptive response that defines a circulating metabolomic signature in ischemic stroke patients. J Cereb Blood Flow Metab 2022; 42:2201-2215. [PMID: 35869638 PMCID: PMC9670009 DOI: 10.1177/0271678x221116288] [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] [Indexed: 12/14/2022]
Abstract
Transient ischemic attacks (TIAs) before an acute ischemic stroke (AIS) could induce ischemic tolerance (IT) phenomena. with an endogenous neuroprotective role (Ischemic preconditioning. IPC). A consecutive prospective cohort of patients with AIS were recruited from 8 different hospitals. Participants were classified by those with non-previous recent TIA vs. previous TIA (within seven days. TIA ≤7d). A total of 541 AIS patients were recruited. 40 (7.4%). of them had previous TIA ≤7d. In line with IPC. patients with TIA ≤7d showed: 1) a significantly less severe stroke at admission by NIHSS score. 2) a better outcome at 7-90 days follow-up and reduced infarct volumes. 3) a specific upregulated metabolomics/lipidomic profile composed of diverse lipid categories. Effectively. IPC activates an additional adaptive response on increasing circulation levels of structural and bioactive lipids to facilitate functional recovery after AIS which may support biochemical machinery for neuronal survival. Furthermore. previous TIA before AIS seems to facilitate the production of anti-inflammatory mediators that contribute to a better immune response. Thus. the IT phenomena contributes to a better adaptation of further ischemia. Our study provides first-time evidence of a metabolomics/lipidomic signature related to the development of stroke tolerance in AIS patients induced by recent TIA.
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Affiliation(s)
- Joaquim Sol
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain.,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
| | - Laura Colàs-Campàs
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain
| | - Gerard Mauri-Capdevila
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain.,Stroke Unit, Department of Neurology, Hospital Universitari Arnau de Vilanova de Lleida, Lleida, Spain
| | - Jessica Molina-Seguin
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain
| | - José Daniel Galo-Licona
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Coral Torres-Querol
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain
| | | | | | | | - Silvia Tur
- Son Espases Hospital, Palma de Mallorca, Spain
| | | | | | | | - Tomás Segura
- Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Reinald Pamplona
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Manel Portero-Otín
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Gloria Arqué
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain
| | - Mariona Jové
- Experimental Medicine Department, Lleida University-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Francisco Purroy
- Clinical Neurosciences Group, Institut de Recerca Biomèdica de Lleida, UdL, Lleida, Spain.,Stroke Unit, Department of Neurology, Hospital Universitari Arnau de Vilanova de Lleida, Lleida, Spain
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88
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High-Resolution Magic-Angle-Spinning NMR in Revealing Hepatoblastoma Hallmarks. Biomedicines 2022; 10:biomedicines10123091. [PMID: 36551847 PMCID: PMC9775661 DOI: 10.3390/biomedicines10123091] [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: 11/02/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
Cancer is one of the leading causes of death in children and adolescents worldwide; among the types of liver cancer, hepatoblastoma (HBL) is the most common in childhood. Although it affects only two to three individuals in a million, it is mostly asymptomatic at diagnosis, so by the time it is detected it has already advanced. There are specific recommendations regarding HBL treatment, and ongoing studies to stratify the risks of HBL, understand the pathology, and predict prognostics and survival rates. Although magnetic resonance imaging spectroscopy is frequently used in diagnostics of HBL, high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy of HBL tissues is scarce. Using this technique, we studied the alterations among tissue metabolites of ex vivo samples from (a) HBL and non-cancer liver tissues (NCL), (b) HBL and adjacent non-tumor samples, and (c) two regions of the same HBL samples, one more centralized and the other at the edge of the tumor. It was possible to identify metabolites in HBL, then metabolites from the HBL center and the border samples, and link them to altered metabolisms in tumor tissues, highlighting their potential as biochemical markers. Metabolites closely related to liver metabolisms such as some phospholipids, triacylglycerides, fatty acids, glucose, and amino acids showed differences between the tissues.
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89
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Hohenwallner K, Troppmair N, Panzenboeck L, Kasper C, El Abiead Y, Koellensperger G, Lamp LM, Hartler J, Egger D, Rampler E. Decoding Distinct Ganglioside Patterns of Native and Differentiated Mesenchymal Stem Cells by a Novel Glycolipidomics Profiling Strategy. JACS AU 2022; 2:2466-2480. [PMID: 36465531 PMCID: PMC9709940 DOI: 10.1021/jacsau.2c00230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 06/17/2023]
Abstract
Gangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. We demonstrated the high-throughput universal capability of our novel analytical strategy by identifying 254 ganglioside species. As a proof of concept, 137 unique gangliosides were annotated in native and differentiated human mesenchymal stem cells including 78 potential cell-state-specific markers and 38 previously unreported gangliosides. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. The combination of the developed glycolipidomics assay with the extended automated annotation tool enables comprehensive in-depth ganglioside characterization as shown on biological samples of interest. Our results suggest ganglioside patterns as a promising quality control tool for stem cells and their differentiation products. Additionally, we believe that our analytical workflow paves the way for probing glycolipid-based biochemical processes shedding light on the enigmatic processes of gangliosides and glycolipids in general.
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Affiliation(s)
- Katharina Hohenwallner
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Nina Troppmair
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Lisa Panzenboeck
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Cornelia Kasper
- Institute
of Cell and Tissue Culture Technologies, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Yasin El Abiead
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Gunda Koellensperger
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Leonida M. Lamp
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
| | - Jürgen Hartler
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
- Field
of Excellence BioHealth − University
of Graz, Graz 8010, Austria
| | - Dominik Egger
- Institute
of Cell and Tissue Culture Technologies, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Evelyn Rampler
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
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90
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Galal A, Talal M, Moustafa A. Applications of machine learning in metabolomics: Disease modeling and classification. Front Genet 2022; 13:1017340. [PMID: 36506316 PMCID: PMC9730048 DOI: 10.3389/fgene.2022.1017340] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Metabolomics research has recently gained popularity because it enables the study of biological traits at the biochemical level and, as a result, can directly reveal what occurs in a cell or a tissue based on health or disease status, complementing other omics such as genomics and transcriptomics. Like other high-throughput biological experiments, metabolomics produces vast volumes of complex data. The application of machine learning (ML) to analyze data, recognize patterns, and build models is expanding across multiple fields. In the same way, ML methods are utilized for the classification, regression, or clustering of highly complex metabolomic data. This review discusses how disease modeling and diagnosis can be enhanced via deep and comprehensive metabolomic profiling using ML. We discuss the general layout of a metabolic workflow and the fundamental ML techniques used to analyze metabolomic data, including support vector machines (SVM), decision trees, random forests (RF), neural networks (NN), and deep learning (DL). Finally, we present the advantages and disadvantages of various ML methods and provide suggestions for different metabolic data analysis scenarios.
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Affiliation(s)
- Aya Galal
- Systems Genomics Laboratory, American University in Cairo, New Cairo, Egypt,Institute of Global Health and Human Ecology, American University in Cairo, New Cairo, Egypt
| | - Marwa Talal
- Systems Genomics Laboratory, American University in Cairo, New Cairo, Egypt,Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo, Egypt,Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt,Department of Biology, American University in Cairo, New Cairo, Egypt,*Correspondence: Ahmed Moustafa,
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91
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Processes in DNA damage response from a whole-cell multi-omics perspective. iScience 2022; 25:105341. [PMID: 36339253 PMCID: PMC9633746 DOI: 10.1016/j.isci.2022.105341] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Technological advances have made it feasible to collect multi-condition multi-omic time courses of cellular response to perturbation, but the complexity of these datasets impedes discovery due to challenges in data management, analysis, visualization, and interpretation. Here, we report a whole-cell mechanistic analysis of HL-60 cellular response to bendamustine. We integrate both enrichment and network analysis to show the progression of DNA damage and programmed cell death over time in molecular, pathway, and process-level detail using an interactive analysis framework for multi-omics data. Our framework, Mechanism of Action Generator Involving Network analysis (MAGINE), automates network construction and enrichment analysis across multiple samples and platforms, which can be integrated into our annotated gene-set network to combine the strengths of networks and ontology-driven analysis. Taken together, our work demonstrates how multi-omics integration can be used to explore signaling processes at various resolutions and demonstrates multi-pathway involvement beyond the canonical bendamustine mechanism.
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92
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Guo P, Teng T, Liu W, Fang Y, Wei B, Feng J, Huang H. Metabolomic analyses redefine the biological classification of pancreatic cancer and correlate with clinical outcomes. Int J Cancer 2022; 151:1835-1846. [PMID: 35830200 DOI: 10.1002/ijc.34208] [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: 03/23/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by high heterogeneity, and the postoperative prognosis of different patients often varies greatly. Therefore, the classification of pancreatic cancer patients and precise treatment becomes particularly important. In our study, 1 H NMR spectroscopy was used to analyze the 76 PDAC serum samples and identify the potential metabolic subtypes. The metabolic characteristics of each metabolic subtype were screened out and the relationship between metabolic subtype and the long-term prognosis was further identified. The clinical stages of PDAC did not show the metabolic differences at the serum metabolomic level. And three metabolic subtypes, basic, choline-like and amino acid-enriched types, were defined by the hierarchical cluster analysis of the serum metabolites and the disturbed metabolic pathways. The characteristic metabolites of each PDAC subtype were identified, and the metabolite model was established to distinguish the PDAC patients in the different subtypes. Among the three metabolic subtypes, choline-like type displayed better long-term prognosis compared to the other two types of patients. Metabolic subtypes are of clinical importance and are closer to expressing the heterogeneity in the actual life activities of pancreatic cancer than molecular typing. The excavation of metabolic subtypes based on this will be more in line with clinical reality and more promising to guide clinical precision individualization treatment.
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Affiliation(s)
- Pengfei Guo
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Tianhong Teng
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Wuping Liu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Yanying Fang
- Fuzhou Children Hospital of Fujian Province, Fuzhou, China
| | - Binbin Wei
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Heguang Huang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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93
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Metabolomic Profiles on Antiblastic Cardiotoxicity: New Perspectives for Early Diagnosis and Cardioprotection. J Clin Med 2022; 11:jcm11226745. [PMID: 36431222 PMCID: PMC9693331 DOI: 10.3390/jcm11226745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Antiblastic drugs-induced cardiomyopathy remains a relevant cause of morbidity and mortality, during and after chemotherapy, despite the progression in protective therapy against cardiovascular diseases and myocardial function. In the last few decades, many groups of researchers have focused their attention on studying the metabolic profile, first in animals, and, subsequently, in humans, looking for profiles which could be able to predict drug-induced cardiotoxicity and cardiovascular damage. In clinical practice, patients identified as being at risk of developing cardiotoxicity undergo a close follow-up and more tailored therapies. Injury to the heart can be a consequence of both new targeted therapies, such as tyrosine kinase inhibitors, and conventional chemotherapeutic agents, such as anthracyclines. This review aims to describe all of the studies carried on this topic of growing interest.
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94
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Meintani DG, Chatzimitakos TG, Kasouni AI, Stalikas CD. Untargeted metabolomics of human keratinocytes reveals the impact of exposure to 2,6-dichloro-1,4-benzoquinone and 2,6-dichloro-3-hydroxy-1,4-benzoquinone as emerging disinfection by-products. Metabolomics 2022; 18:89. [PMID: 36342571 PMCID: PMC9640400 DOI: 10.1007/s11306-022-01935-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022]
Abstract
INTRODUCTION The 2,6-dichloro-1,4-benzoquinone (DCBQ) and its derivative 2,6-dichloro-3-hydroxy-1,4-benzoquinone (DCBQ-OH) are disinfection by-products (DBPs) and emerging pollutants in the environment. They are considered to be of particular importance as they have a high potential of toxicity and they are likely to be carcinogenic. OBJECTIVES In this study, human epidermal keratinocyte cells (HaCaT) were exposed to the DCBQ and its derivative DCBQ-OH, at concentrations equivalent to their IC20 and IC50, and a study of the metabolic phenotype of cells was performed. METHODS The perturbations induced in cellular metabolites and their relative content were screened and evaluated through a metabolomic study, using 1H-NMR and MS spectroscopy. RESULTS Changes in the metabolic pathways of HaCaT at concentrations corresponding to IC20 and IC50 of DCBQ-OH involved the activation of cell membrane α-linolenic acid, biotin, and glutathione and deactivation of glycolysis/gluconeogenesis at IC50. The changes in metabolic pathways at IC20 and IC50 of DCBQ were associated with the activation of inositol phosphate, pertaining to the transfer of messages from the receptors of the membrane to the interior as well as with riboflavin. Deactivation of biotin metabolism was recorded, among others. The cells exposed to DCBQ exhibited a concentration-dependent decrease in saccharide concentrations. The concentration of steroids increased when cells were exposed to IC20 and decreased at IC50. Although both chemical factors stressed the cells, DCBQ led to the activation of transporting messages through phosphorylated derivatives of inositol. CONCLUSION Our findings provided insights into the impact of the two DBPs on human keratinocytes. Both chemical factors induced energy production perturbations, oxidative stress, and membrane damage.
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Affiliation(s)
- Dimitra G Meintani
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece
| | - Theodoros G Chatzimitakos
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece
| | - Athanasia I Kasouni
- Laboratory of Biophysical Chemistry, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
| | - Constantine D Stalikas
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece.
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95
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Pharmacometabolomic study of drug response to antihypertensive medications for hypertension marker identification in Han Chinese individuals in Taiwan. Comput Struct Biotechnol J 2022; 20:6458-6466. [DOI: 10.1016/j.csbj.2022.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/13/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
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96
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Lee DY, Kim JY, Ahn E, Hyeon JS, Kim GH, Park KJ, Jung Y, Lee YJ, Son MK, Kim SW, Han SY, Kim JH, Roh GS, Cha DR, Hwang GS, Kim WH. Associations between local acidosis induced by renal LDHA and renal fibrosis and mitochondrial abnormalities in patients with diabetic kidney disease. Transl Res 2022; 249:88-109. [PMID: 35788054 DOI: 10.1016/j.trsl.2022.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/23/2022] [Accepted: 06/22/2022] [Indexed: 10/31/2022]
Abstract
During the progression of diabetic kidney disease (DKD), renal lactate metabolism is rewired. The relationship between alterations in renal lactate metabolism and renal fibrosis in patients with diabetes has only been partially established due to a lack of biopsy tissues from patients with DKD and the intricate mechanism of lactate homeostasis. The role of lactate dehydrogenase A (LDHA)-mediated lactate generation in renal fibrosis and dysfunction in human and animal models of DKD was explored in this study. Measures of lactate metabolism (urinary lactate levels and LDHA expression) and measures of DKD progression (estimated glomerular filtration rate and Wilms' tumor-1 expression) were strongly negatively correlated in patients with DKD. Experiments with streptozotocin-induced DKD rat models and the rat renal mesangial cell model confirmed our findings. We found that the pathogenesis of DKD is linked to hypoxia-mediated lactic acidosis, which leads to fibrosis and mitochondrial abnormalities. The pathogenic characteristics of DKD were significantly reduced when aerobic glycolysis or LDHA expression was inhibited. Further studies will aim to investigate whether local acidosis caused by renal LDHA might be exploited as a therapeutic target in patients with DKD.
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Affiliation(s)
- Dae-Yeon Lee
- Division of Cardiovascular Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea; Department of Anatomy and Convergence Medical Science, Bio Anti-aging Medical Research Center, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Republic of Korea
| | - Ji-Yeon Kim
- Division of Cardiovascular Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Eunyong Ahn
- Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Jin Seong Hyeon
- Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Gyu-Hee Kim
- Division of Metabolic Disease Research, Department for Chronic Disease Convergence Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Keon-Jae Park
- Division of Metabolic Disease Research, Department for Chronic Disease Convergence Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Youngae Jung
- Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Yoo-Jeong Lee
- Division of Metabolic Disease Research, Department for Chronic Disease Convergence Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Mi Kyoung Son
- Division of Cardiovascular Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Seung Woo Kim
- Division of Cardiovascular Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Sang Youb Han
- Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, Republic of Korea
| | - Jae-Hong Kim
- Division of Life Sciences, College of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Gu Seob Roh
- Department of Anatomy and Convergence Medical Science, Bio Anti-aging Medical Research Center, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Republic of Korea
| | - Dae Ryong Cha
- Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Republic of Korea.
| | - Geum-Sook Hwang
- Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea.
| | - Won-Ho Kim
- Division of Cardiovascular Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea.
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97
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Longitudinal metabolomic profiles reveal sex-specific adjustments to long-duration spaceflight and return to Earth. Cell Mol Life Sci 2022; 79:578. [DOI: 10.1007/s00018-022-04566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/05/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022]
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98
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Molecular Classification of Genes Associated with Hypoxic Lipid Metabolism in Pancreatic Cancer. Biomolecules 2022; 12:biom12101533. [PMID: 36291742 PMCID: PMC9599075 DOI: 10.3390/biom12101533] [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: 09/13/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Abnormal lipid metabolism often occurs under hypoxic microenvironment, which is an important energy supplement for cancer cell proliferation and metastasis. We aimed to explore the lipid metabolism characteristics and gene expression features of pancreatic ductal adenocarcinoma (PDAC) related to hypoxia and identify biomarkers for molecular classification based on hypoxic lipid metabolism that are evaluable for PDAC prognosis and therapy. The multiple datasets were analyzed integratively, including corresponding clinical information of samples. PDAC possesses a distinct metabolic profile and oxygen level compared with normal pancreatic tissues, according to the bioinformatics methods. In addition, a study on untargeted metabolomics using Ultra Performance Liquid Chromatography Tandem Mass Spectrometry(UPLC-MS) revealed lipid metabolites differences affected by oxygen. Analysis of PDAC gene expression profiling in The Cancer Genome Atlas (TCGA) revealed that the sphingolipid process correlates closely with HIF1α. According to the characters of HIF-1 and sphingolipid, samples can be clustered into three subgroups using non-negative matrix factorization clustering. In cluster2, patients had an increased survival time. Relatively high MUC16 mutation arises in cluster2 and may positively influence the cancer survival rates. This study explored the expression pattern of lipid metabolism under hypoxia microenvironment in PDAC. On the basis of metabolic signatures, we identified the prognosis subtypes linking lipid metabolism to hypoxia. The classifications may be conducive to developing personalized treatment programs targeting metabolic profiles.
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99
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Ferrante L, Rajpoot K, Jeeves M, Ludwig C. Automated analysis for multiplet identification from ultra-high resolution 2D-1H,13C-HSQC NMR spectra. Wellcome Open Res 2022; 7:262. [PMID: 37008249 PMCID: PMC10050905 DOI: 10.12688/wellcomeopenres.18248.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D-1H,13C-HSQC NMR spectra arising from 13C -13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D-1H,13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D-1H,13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
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Affiliation(s)
- Laura Ferrante
- School of Computer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kashif Rajpoot
- University of Birmingham Dubai, Dubai International Academic City, United Arab Emirates
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK
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100
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Bocsa DC, Socaciu C, Iancu SD, Pelea MA, Gutiu RI, Leopold N, Fodor D. Stage related metabolic profile of the synovial fluid in patients with acute flares of knee osteoarthritis. Med Pharm Rep 2022; 95:438-445. [PMID: 36506601 PMCID: PMC9694744 DOI: 10.15386/mpr-2454] [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: 12/15/2021] [Revised: 01/27/2022] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
Background and aim Osteoarthritis (OA) is the most common joint condition and the leading cause of pain and disability in elderly patients. Currently, there is no biomarker available for the early diagnosis of OA, and limited data is available regarding the molecular basis of progression for OA. For this reason, this study aimed to identify the metabolomic profile of early and late OA using high-performance liquid chromatography coupled with untargeted mass spectrometry (LC-MS). Methods 31 patients with knee OA and joint effusion were enrolled. Based on Kellgren/Laurence scale, 12 patients were classified as early OA (eOA) and 19 as late OA (lOA). The synovial fluid (SF) was collected and characterized by untargeted LC-MS. Only the metabolites identified in more than 25% of each group were kept for further analysis. Principal component analysis (PCA) enabled the unsupervised clustering of the eOA and lOA groups. Further, for classification, the best three principal components (PCs) were used as input for two machine learning algorithms (random forest and naïve Bayes), which were trained to discriminate between the eOA and lOA groups. Results 43 metabolites were identified in both eOA and lOA, but after selecting the metabolites present in at least 25% of the patients in each group, the metabolomics analysis yielded a panel of only nine metabolites: four metabolites related to phospholipids (phosphatidylcholine 20:0/18:2 and 18:0/20:2, sphingomyelin, and ceramide), three metabolites belonging to purine metabolites (inosine 5'-phosphate, adenosine thiamine diphosphate, and diadenosine 5',5'-diphosphate), one metabolite was a gonadal steroid hormone (estrone 3-sulfate), and one metabolite represented by heme, with all but ceramide (d18:1/20:0) being enriched in the lOA group. By using as features the best three PCs (PC2, PC8 and PC9), random forest and naïve Bayes machine learning algorithms yielded a classification accuracy of 0.81 and 0.78, respectively. Conclusion Our LC-MS analysis of SF from patients with eOA and lOA indicates stage-dependent differences, lOA being associated with a perturbed metabolome of phospholipids, purine metabolites, gonadal steroid hormones (estrone 3-sulfate) and a heme molecule. Specific questions need to be answered regarding the biosynthesis and function of these metabolites in osteoarthritic joints, with the aim of developing new relevant biomarkers and therapeutic strategies.
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Affiliation(s)
- Delia-Corina Bocsa
- 2 Internal Medicine Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Carmen Socaciu
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania,BIODIATECH - Research Center for Applied Biotechnology in Diagnosis and Molecular Therapy, Cluj-Napoca, Romania
| | | | - Michael Andrei Pelea
- 2 Internal Medicine Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Roxana Ioana Gutiu
- 2 Internal Medicine Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Daniela Fodor
- 2 Internal Medicine Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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