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Zhang M, Shi F, Chen Y, Yang C, Zhang X, Deng C, Sun N. Straightforward Creation of Multishell Hollow Hybrids for an Integrated Metabolic Monitoring System in Disease Management. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400941. [PMID: 38529737 DOI: 10.1002/smll.202400941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Multidimensional metabolic analysis has become a new trend in establishing efficient disease monitoring systems, as the constraints associated with relying solely on a single dimension in refined monitoring are increasingly pronounced. Here, coordination polymers are employed as derivative precursors to create multishell hollow hybrids, developing an integrated metabolic monitoring system. Briefly, metabolic fingerprints are extracted from hundreds of serum samples and urine samples, encompassing not only membranous nephropathy but also related diseases, using high-throughput mass spectrometry. With optimized algorithm and initial feature selection, the established combined panel demonstrates enhanced accuracy in both subtype differentiation (over 98.1%) and prognostic monitoring (over 95.6%), even during double blind test. This surpasses the serum biomarker panel (≈90.7% for subtyping, ≈89.7% for prognosis) and urine biomarker panel (≈94.4% for subtyping, ≈76.5% for prognosis). Moreover, after attempting to further refine the marker panel, the blind test maintains equal sensitivity, specificity, and accuracy, showcasing a comprehensive improvement over the single-fluid approach. This underscores the remarkable effectiveness and superiority of the integrated strategy in discriminating between MN and other groups. This work has the potential to significantly advance diagnostic medicine, leading to the establishment of more effective strategies for patient management.
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Affiliation(s)
- Man Zhang
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Fangying Shi
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yijie Chen
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Chenyu Yang
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Chunhui Deng
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
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2
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Victor Oluwaloseyi A, Aduragbemi Noah O, Lydia Oluwatoyin A, Gaffar Y, Moses O, Oyedayo Phillips A, Comfort Onaolapo M, Sylvester Olateju B, Ademola Ayodele A, Mega Obukohwo O, Ayodeji Folorunsho A. Metabolomics of male infertility. Clin Chim Acta 2024; 556:117850. [PMID: 38431200 DOI: 10.1016/j.cca.2024.117850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
This review explores the use of metabolomics in male infertility. Metabolomics, an evolving omics technology that targets the products of cellular metabolism, is valuable for elucidating underlying pathophysiology of many disorders including male infertility. The identification of reliable biomarkers is essential for accurate diagnosis and for developing precision therapeutics for those afflicted by reproductive dysfunction. Unfortunately, despite significant progress to date, the intricate relationships between these metabolic pathways and male infertility remain elusive. It is clear, however, that additional research is required to more fully characterize the role of metabolomics in this disorder and in the potential development of targeted therapies for precision medicine.
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Affiliation(s)
- Amos Victor Oluwaloseyi
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria
| | - Odeyemi Aduragbemi Noah
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Ajayi Lydia Oluwatoyin
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Yusuff Gaffar
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olotu Moses
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Moyinoluwa Comfort Onaolapo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria
| | | | - Adelakun Ademola Ayodele
- Department of Medical Laboratory Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Ajayi Ayodeji Folorunsho
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Adeleke University, Ede, Osun State, Nigeria.
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3
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Jia K, Wang Y, Jiang L, Lai M, Liu W, Wang L, Liu H, Cao X, Li Y, Nie Z. Urine Metabolic Profiling for Rapid Lung Cancer Screening: A Strategy Combining Rh-Doped SrTiO 3-Assisted Laser Desorption/Ionization Mass Spectrometry and Machine Learning. ACS APPLIED MATERIALS & INTERFACES 2024; 16:12302-12309. [PMID: 38414269 DOI: 10.1021/acsami.3c19007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Lung cancer ranks among the cancers with the highest global incidence rates and mortality. Swift and extensive screening is crucial for the early-stage diagnosis of lung cancer. Laser desorption/ionization mass spectrometry (LDI-MS) possesses clear advantages over traditional analytical methods for large-scale analysis due to its unique features, such as simple sample processing, rapid speed, and high-throughput performance. As n-type semiconductors, titanate-based perovskite materials can generate charge carriers under ultraviolet light irradiation, providing the capability for use as an LDI-MS substrate. In this study, we employ Rh-doped SrTiO3 (STO/Rh)-assisted LDI-MS combined with machine learning to establish a method for urine-based lung cancer screening. We directly analyzed urine metabolites from lung cancer patients (LCs), pneumonia patients (PNs), and healthy controls (HCs) without employing any pretreatment. Through the integration of machine learning, LCs are successfully distinguished from HCs and PNs, achieving impressive area under the curve (AUC) values of 0.940 for LCs vs HCs and 0.864 for LCs vs PNs. Furthermore, we identified 10 metabolites with significantly altered levels in LCs, leading to the discovery of related pathways through metabolic enrichment analysis. These results suggest the potential of this method for rapidly distinguishing LCs in clinical applications and promoting precision medicine.
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Affiliation(s)
- Ke Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemistry and Chemical Engineering, Jiangxi Province Engineering Research Center of Ecological Chemical Industry, Jiujiang University, Jiujiang, Jiangxi 332005, China
| | - Lixia Jiang
- Gannan Medical University, Ganzhou 341000, China
| | - Mi Lai
- Gannan Medical University, Ganzhou 341000, China
| | - Wenlan Liu
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Liping Wang
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohua Cao
- School of Chemistry and Chemical Engineering, Jiangxi Province Engineering Research Center of Ecological Chemical Industry, Jiujiang University, Jiujiang, Jiangxi 332005, China
| | - Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Zheng H, Wang C, Yu X, Zheng W, An Y, Zhang J, Zhang Y, Wang G, Qi M, Lin H, Wang F. The Role of Metabolomics and Microbiology in Urinary Tract Infection. Int J Mol Sci 2024; 25:3134. [PMID: 38542107 PMCID: PMC10969911 DOI: 10.3390/ijms25063134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 08/25/2024] Open
Abstract
One of the common illnesses that affect women's physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient's urine in relation to their role in supporting host health.
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Affiliation(s)
- Haoyu Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Chao Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Xiao Yu
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Wenxue Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Yiming An
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Jiaqi Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Yuhan Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Guoqiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Mingran Qi
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Hongqiang Lin
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
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5
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Lim H, Lee S, Jin JS, Kim MS. High-Throughput Quantitative Analysis of Amino Acids in Freeze-Dried Drops Using Time-of-Flight Secondary Ion Mass Spectrometry. Anal Chem 2024; 96:3717-3721. [PMID: 38262943 DOI: 10.1021/acs.analchem.3c04855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a promising analytical tool for molecular profiling in biological applications. However, its ultrahigh vacuum environment and matrix effects hamper the absolute quantitation of solution samples. Herein, we present a rapid high-throughput platform for quantitative ToF-SIMS analysis of amino acids in matrix deposits formed from freeze-dried solution drops through ice sublimation on a parylene film microarray substrate. Droplets of the amino acid solutions, which were mixed with stable isotope-labeled phenylalanine (F*) of high concentration (10 mM), were loaded on wells of the microarray, then frozen and evaporated slowly below the freezing point, forming continuous solid-phase F* matrix deposits. The amino acids (≤500 μM), adequately well dispersed throughout the F* matrix deposits on each well, were quantitatively analyzed by ToF-SIMS in a rapid and high-throughput fashion. The lower limit of quantitation reached below 10 μM.
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Affiliation(s)
- Heejin Lim
- Center for Scientific Instrumentation, Korea Basic Science Institute (KBSI), Cheongju 28119, Republic of Korea
| | - Siheun Lee
- School of Undergraduate Studies, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jong Sung Jin
- Busan Center, Korea Basic Science Institute (KBSI), Busan 46742, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- Center for Cell Fate Reprogramming and Control, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
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6
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António M, Vitorino R, Daniel-da-Silva AL. LSPR-Based Aptasensor for Rapid Urinary Detection of NT-proBNP. BIOSENSORS 2023; 13:736. [PMID: 37504134 PMCID: PMC10377000 DOI: 10.3390/bios13070736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
N-terminal pro-brain natriuretic peptide (NT-proBNP) is a myocardial stress biomarker that can be found in serum or plasma, saliva, and urine in the context of cardiovascular disease. In this study, we developed a rapid (~25 min) and straightforward localized surface plasmon resonance (LSPR)-based assay for detecting NT-proBNP in urine. The assay employs citrate-capped gold nanoparticles (AuNPs) and an aptamer specific for NT-proBNP, which initially interacts with NT-proBNP. The remaining unbound aptamer then interacts with the AuNPs, and the addition of NaCl induces the aggregation of the unprotected AuNPs, resulting in a decrease in absorbance at the LSPR band (A521) and an increase in absorbance at 750 nm (A750). The concentration of NT-proBNP showed a linear correlation with the aggregation ratio (A521/A750), and the assay demonstrated a limit of detection (LOD) of 0.303 µg·L-1 and a detection range of 0.566-8 µg·L-1. However, the presence of sulfur-containing proteins in saliva and fetal bovine serum hindered the detection of NT-proBNP in these biofluids. Nevertheless, the assay successfully detected NT-proBNP in diluted urine with an LOD of 0.417 µg·L-1 and a detection range of 0.589-6 µg·L-1. The observed values in urine samples from preterm infants with cardiovascular disease fell within this range, indicating the potential clinical relevance of the assay. The recovery percentages ranged from 92.3 to 116.3%. Overall, our findings suggest that the LSPR-based assay for NT-proBNP detection in urine can be a valuable tool for the diagnosis and treatment of cardiovascular disease.
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Affiliation(s)
- Maria António
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- LAQV-REQUIMTE, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- UnIC@RISE, Department of Surgery and Physiology, Cardiovascular R&D Center, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ana L Daniel-da-Silva
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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Hotea I, Sirbu C, Plotuna AM, Tîrziu E, Badea C, Berbecea A, Dragomirescu M, Radulov I. Integrating (Nutri-)Metabolomics into the One Health Tendency-The Key for Personalized Medicine Advancement. Metabolites 2023; 13:800. [PMID: 37512507 PMCID: PMC10384896 DOI: 10.3390/metabo13070800] [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: 06/15/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Metabolomics is an advanced technology, still under development, with multiple research applications, especially in the field of health. Individual metabolic profiles, the functionality of the body, as well as its interaction with the environment, can be established using this technology. The body's response to various external factors, including the food consumed and the nutrients it contains, has increased researchers' interest in nutrimetabolomics. Establishing correlations between diet and the occurrence of various diseases, or even the development of personalized nutrition plans, could contribute to advances in precision medicine. The interdependence between humans, animals, and the environment is of particular importance today, with the dramatic emergence and spread of zoonotic diseases, food, water and soil contamination, and the degradation of resources and habitats. All these events have led to an increase in risk factors for functional diseases, burdening global health. Thus, this study aimed to highlight the importance of metabolomics, and, in particular, nutrimetabolomics, as a technical solution for a holistic, collaborative, and precise approach for the advancement of the One Health strategy.
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Affiliation(s)
- Ionela Hotea
- Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Catalin Sirbu
- Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Ana-Maria Plotuna
- Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Emil Tîrziu
- Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Corina Badea
- Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Adina Berbecea
- Faculty of Agriculture, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Monica Dragomirescu
- Faculty of Bioengineering of Animal Resources, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
| | - Isidora Radulov
- Faculty of Agriculture, University of Life Sciences "King Mihai I" from Timisoara, Calea Aradului, No. 119, 300645 Timisoara, Romania
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Madrid-Gambin F, Oller S, Marco S, Pozo ÓJ, Andres-Lacueva C, Llorach R. Quantitative plasma profiling by 1H NMR-based metabolomics: impact of sample treatment. Front Mol Biosci 2023; 10:1125582. [PMID: 37333016 PMCID: PMC10273206 DOI: 10.3389/fmolb.2023.1125582] [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: 12/16/2022] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction: There is evidence that sample treatment of blood-based biosamples may affect integral signals in nuclear magnetic resonance-based metabolomics. The presence of macromolecules in plasma/serum samples makes investigating low-molecular-weight metabolites challenging. It is particularly relevant in the targeted approach, in which absolute concentrations of selected metabolites are often quantified based on the area of integral signals. Since there are a few treatments of plasma/serum samples for quantitative analysis without a universally accepted method, this topic remains of interest for future research. Methods: In this work, targeted metabolomic profiling of 43 metabolites was performed on pooled plasma to compare four methodologies consisting of Carr-Purcell-Meiboom-Gill (CPMG) editing, ultrafiltration, protein precipitation with methanol, and glycerophospholipid solid-phase extraction (g-SPE) for phospholipid removal; prior to NMR metabolomics analysis. The effect of the sample treatments on the metabolite concentrations was evaluated using a permutation test of multiclass and pairwise Fisher scores. Results: Results showed that methanol precipitation and ultrafiltration had a higher number of metabolites with coefficient of variation (CV) values above 20%. G-SPE and CPMG editing demonstrated better precision for most of the metabolites analyzed. However, differential quantification performance between procedures were metabolite-dependent. For example, pairwise comparisons showed that methanol precipitation and CPMG editing were suitable for quantifying citrate, while g-SPE showed better results for 2-hydroxybutyrate and tryptophan. Discussion: There are alterations in the absolute concentration of various metabolites that are dependent on the procedure. Considering these alterations is essential before proceeding with the quantification of treatment-sensitive metabolites in biological samples for improving biomarker discovery and biological interpretations. The study demonstrated that g-SPE and CPMG editing are effective methods for removing proteins and phospholipids from plasma samples for quantitative NMR analysis of metabolites. However, careful consideration should be given to the specific metabolites of interest and their susceptibility to the sample treatment procedures. These findings contribute to the development of optimized sample preparation protocols for metabolomics studies using NMR spectroscopy.
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Affiliation(s)
- Francisco Madrid-Gambin
- Applied Metabolomics Research Group, IMIM—Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sergio Oller
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Barcelona, Spain
| | - Santiago Marco
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Barcelona, Spain
| | - Óscar J. Pozo
- Applied Metabolomics Research Group, IMIM—Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Sant Coloma de Gramanet, Spain
- Food Innovation Network (XIA), Santa Coloma de Gramanet, Spain
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB), Santa Coloma de Gramanet, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Llorach
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Sant Coloma de Gramanet, Spain
- Food Innovation Network (XIA), Santa Coloma de Gramanet, Spain
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB), Santa Coloma de Gramanet, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
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Chowdhury CR, Kavitake D, Jaiswal KK, Jaiswal KS, Reddy GB, Agarwal V, Shetty PH. NMR-based metabolomics as a significant tool for human nutritional research and health applications. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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10
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Chang CW, Hsu JY, Su YH, Chen YC, Hsiao PZ, Liao PC. Monitoring long-term chemical exposome by characterizing the hair metabolome using a high-resolution mass spectrometry-based suspect screening approach. CHEMOSPHERE 2023; 332:138864. [PMID: 37156292 DOI: 10.1016/j.chemosphere.2023.138864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Hair has recently emerged as a biospecimen for characterizing the long-term chemical exposome in biomonitoring investigations spanning several months, as chemical compounds circulating in the bloodstream accumulate in hair. Although there has been interest in using human hair as a biospecimen for exposome studies, it has yet to be widely adopted compared to blood and urine. Here, we applied a high-resolution mass spectrometry (HRMS)-based suspect screening strategy to characterize the long-term chemical exposome in human hair. Hair samples were collected from 70 subjects and cut into 3 cm segments, which were then mixed to prepare pooled samples. The pooled hair samples underwent a sample preparation procedure, and the hair extracts were further analyzed using an HRMS-based suspect screening approach. An in-house chemical suspect list containing 1227 chemical entries from National Report on Human Exposure to Environmental Chemicals (Report) published by the U.S. CDC and the Exposome-Explorer 3.0 database developed by the WHO was subsequently used to screen and filter the suspect features against the HRMS dataset. Overall, we matched 587 suspect features in the HRMS dataset to 246 unique chemical formulas in the suspect list, and the structures of 167 chemicals were further identified through a fragmentation analysis. Among these, chemicals such as mono-2-ethylhexyl phthalate, methyl paraben, and 1-naphthol, which have been detected in the urine or blood for exposure assessment, were also identified in human hair. This suggests that hair reflects the accumulation of environmental compounds to which an individual is exposed. Exposure to exogenous chemicals may exert adverse effects on cognitive function, and we discovered 15 chemicals in human hair that may contribute to the pathogenesis of Alzheimer's disease. This finding suggests that human hair may be a promising biospecimen for monitoring long-term exposure to multiple environmental chemicals and perturbations in endogenous chemicals in biomonitoring investigations.
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Affiliation(s)
- Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Yi Hsu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Hsiang Su
- Division of Neurology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, 60002, Taiwan
| | - Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Zu Hsiao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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11
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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: 37] [Impact Index Per Article: 37.0] [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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12
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Choi S, Ahn DH, Yoo MG, Lee HJ, Cho SB, Park HB, Kim SS, Chu H. Urine Metabolite of Mice with Orientia tsutsugamushi Infection. Am J Trop Med Hyg 2023; 108:296-304. [PMID: 36623483 PMCID: PMC9896320 DOI: 10.4269/ajtmh.20-1608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/23/2022] [Indexed: 01/11/2023] Open
Abstract
Scrub typhus is an acute febrile, mite-borne disease endemic to the Asia-Pacific region. In South Korea, it is a seasonal disease that occurs frequently in the autumn, and its incidence has increased steadily. In this study, we used a liquid chromatography and flow injection analysis-tandem mass spectrometry-based targeted urine metabolomics approach to evaluate the host response to Orientia tsutsugamushi infection. Balb/c mice were infected with O. tsutsugamushi Boryong, and their urine metabolite profile was examined. Metabolites that differed significantly between the experimental groups were identified using the Kruskal-Wallis test. Sixty-five differential metabolites were identified. The principal metabolite classes were acylcarnitines, glycerophospholipids, biogenic amines, and amino acids. An ingenuity pathway analysis revealed that several toxic (cardiotoxic, hepatotoxic, and nephrotoxic) metabolites are induced by scrub typhus infection. This is the first report of urinary metabolite biomarkers of scrub typhus infection and it enhances our understanding of the metabolic pathways involved.
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Affiliation(s)
- Sangho Choi
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Do-Hwan Ahn
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Min-Gyu Yoo
- Division of Endocrine and Kidney Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Hye-Ja Lee
- Division of Endocrine and Kidney Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Seong Beom Cho
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Hee-Bin Park
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Sung Soon Kim
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
| | - Hyuk Chu
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, Osong-eup, Cheongju-si, Chungcheongbuk-do, 28160, Republic of Korea
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13
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Huang Z, Yang X, Huang Y, Tang Z, Chen Y, Liu H, Huang M, Qing L, Li L, Wang Q, Jie Z, Jin X, Jia B. Saliva - a new opportunity for fluid biopsy. Clin Chem Lab Med 2023; 61:4-32. [PMID: 36285724 DOI: 10.1515/cclm-2022-0793] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022]
Abstract
Saliva is a complex biological fluid with a variety of biomolecules, such as DNA, RNA, proteins, metabolites and microbiota, which can be used for the screening and diagnosis of many diseases. In addition, saliva has the characteristics of simple collection, non-invasive and convenient storage, which gives it the potential to replace blood as a new main body of fluid biopsy, and it is an excellent biological diagnostic fluid. This review integrates recent studies and summarizes the research contents of salivaomics and the research progress of saliva in early diagnosis of oral and systemic diseases. This review aims to explore the value and prospect of saliva diagnosis in clinical application.
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Affiliation(s)
- Zhijie Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Xiaoxia Yang
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yisheng Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhengming Tang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yuanxin Chen
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Hongyu Liu
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Mingshu Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Ling Qing
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Li Li
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Qin Wang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhuye Jie
- BGI Genomics, BGI-Shenzhen, Shenzhen, P.R. China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, P.R. China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, P.R. China
| | - Bo Jia
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
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14
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Costantini S, Di Gennaro E, Capone F, De Stefano A, Nasti G, Vitagliano C, Setola SV, Tatangelo F, Delrio P, Izzo F, Avallone A, Budillon A. Plasma metabolomics, lipidomics and cytokinomics profiling predict disease recurrence in metastatic colorectal cancer patients undergoing liver resection. Front Oncol 2023; 12:1110104. [PMID: 36713567 PMCID: PMC9875807 DOI: 10.3389/fonc.2022.1110104] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Purpose In metastatic colorectal cancer (mCRC) patients (pts), treatment strategies integrating liver resection with induction chemotherapy offer better 5-year survival rates than chemotherapy alone. However, liver resection is a complex and costly procedure, and recurrence occurs in almost 2/3rds of pts, suggesting the need to identify those at higher risk. The aim of this work was to evaluate whether the integration of plasma metabolomics and lipidomics combined with the multiplex analysis of a large panel of plasma cytokines can be used to predict the risk of relapse and other patient outcomes after liver surgery, beyond or in combination with clinical morphovolumetric criteria. Experimental design Peripheral blood metabolomics and lipidomics were performed by 600 MHz NMR spectroscopy on plasma from 30 unresectable mCRC pts treated with bevacizumab plus oxaliplatin-based regimens within the Obelics trial (NCT01718873) and subdivided into responder (R) and non-R (NR) according to 1-year disease-free survival (DFS): ≥ 1-year (R, n = 12) and < 1-year (NR, n = 18). A large panel of cytokines, chemokines, and growth factors was evaluated on the same plasma using Luminex xMAP-based multiplex bead-based immunoassay technology. A multiple biomarkers model was built using a support vector machine (SVM) classifier. Results Sparse partial least squares discriminant analysis (sPLS-DA) and loading plots obtained by analyzing metabolomics profiles of samples collected at the time of response evaluation when resectability was established showed significantly different levels of metabolites between the two groups. Two metabolites, 3-hydroxybutyrate and histidine, significantly predicted DFS and overall survival. Lipidomics analysis confirmed clear differences between the R and NR pts, indicating a statistically significant increase in lipids (cholesterol, triglycerides and phospholipids) in NR pts, reflecting a nonspecific inflammatory response. Indeed, a significant increase in proinflammatory cytokines was demonstrated in NR pts plasma. Finally, a multiple biomarkers model based on the combination of presurgery plasma levels of 3-hydroxybutyrate, cholesterol, phospholipids, triglycerides and IL-6 was able to correctly classify patients by their DFS with good accuracy. Conclusion Overall, this exploratory study suggests the potential of these combined biomarker approaches to predict outcomes in mCRC patients who are candidates for liver metastasis resection after induction treatment for defining personalized management and treatment strategies.
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Affiliation(s)
- Susan Costantini
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Elena Di Gennaro
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Francesca Capone
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Alfonso De Stefano
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Guglielmo Nasti
- Innovative Therapy for Abdominal Metastases Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Carlo Vitagliano
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Sergio Venanzio Setola
- Radiology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Fabiana Tatangelo
- Pathology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Paolo Delrio
- Colorectal Oncological Surgery Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Francesco Izzo
- Hepatobiliary Surgery Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Antonio Avallone
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy,*Correspondence: Alfredo Budillon,
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15
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Zhang Y, Liang F, Zhang D, Qi S, Liu Y. Metabolites as extracellular vesicle cargo in health, cancer, pleural effusion, and cardiovascular diseases: An emerging field of study to diagnostic and therapeutic purposes. Biomed Pharmacother 2023; 157:114046. [PMID: 36469967 DOI: 10.1016/j.biopha.2022.114046] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Extracellular vesicles (EVs) are highly diverse nanoscale membrane-bound structures released from different cell types into the extracellular environment. They play essential functions in cell signaling by transporting their cargo, such as proteins, RNA, DNA, lipids, metabolites, and small molecules, to recipient cells. It has recently been shown that EVs might modulate carcinogenesis by delivering cargo to recipient cells. Furthermore, recent discoveries revealed that changes in plasma-derived EV levels and cargo in subjects with metabolic diseases were documented by many researchers, suggesting that EVs might be a promising source of disease biomarkers. One of the cargos of EVs that has recently attracted the most attention is metabolites. The metabolome of these vesicles introduces a plethora of disease indicators; hence, examining the metabolomics of EVs detected in human biofluids would be an effective approach. On the other hand, metabolites have various roles in biological systems, including the production of energies, synthesizing macromolecules, and serving as signaling molecules and hormones. Metabolome rewiring in cancer and stromal cells is a characteristic of malignancy, but the current understanding of how this affects the metabolite composition and activity of tumor-derived EVs remains in its infancy. Since new findings and studies in the field of exosome biology and metabolism are constantly being published, it is likely that diagnostic and treatment techniques, including the use of exosome metabolites, will be launched in the coming years. Recent years have seen increased interest in the EV metabolome as a possible source for biomarker development. However, our understanding of the role of these molecules in health and disease is still immature. In this work, we have provided the latest findings regarding the role of metabolites as EV cargoes in the pathophysiology of diseases, including cancer, pleural effusion (PE), and cardiovascular disease (CVD). We also discussed the significance of metabolites as EV cargoes of microbiota and their role in host-microbe interaction. In addition, the latest findings on metabolites in the form of EV cargoes as biomarkers for disease diagnosis and treatment are presented in this study.
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Affiliation(s)
- Yan Zhang
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Feng Liang
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - DuoDuo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Shuang Qi
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China.
| | - Yan Liu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China.
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16
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Seo SH, Na CS, Park SE, Kim EJ, Kim WS, Park C, Oh S, You Y, Lee MH, Cho KM, Kwon SJ, Whon TW, Roh SW, Son HS. Machine learning model for predicting age in healthy individuals using age-related gut microbes and urine metabolites. Gut Microbes 2023; 15:2226915. [PMID: 37351626 PMCID: PMC10291941 DOI: 10.1080/19490976.2023.2226915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
Age-related gut microbes and urine metabolites were investigated in 568 healthy individuals using metataxonomics and metabolomics. The richness and evenness of the fecal microbiota significantly increased with age, and the abundance of 16 genera differed between the young and old groups. Additionally, 17 urine metabolites contributed to the differences between the young and old groups. Among the microbes that differed by age, Bacteroides and Prevotella 9 were confirmed to be correlated with some urine metabolites. The machine learning algorithm eXtreme gradient boosting (XGBoost) was shown to produce the best performing age predictors, with a mean absolute error of 5.48 years. The accuracy of the model improved to 4.93 years with the inclusion of urine metabolite data. This study shows that the gut microbiota and urine metabolic profiles can be used to predict the age of healthy individuals with relatively good accuracy.
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Affiliation(s)
- Seung-Ho Seo
- Research & Development Team, Sonlab Inc, Seoul, Republic of Korea
| | - Chang-Su Na
- College of Korean Medicine, Dongshin University, Naju, Republic of Korea
| | - Seong-Eun Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Eun-Ju Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Woo-Seok Kim
- Kyurim Korean Medical Clinic, Cheonan, Republic of Korea
| | - ChunKyun Park
- Department of Applied Statistics, Yonsei University, Seoul, Republic of Korea
| | - Seungmi Oh
- Department of Applied Statistics, Yonsei University, Seoul, Republic of Korea
| | - Yanghee You
- College of Korean Medicine, Dongshin University, Naju, Republic of Korea
| | - Mee-Hyun Lee
- College of Korean Medicine, Dongshin University, Naju, Republic of Korea
| | | | | | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Institute, LISCure Biosciences Inc, Seongnam, Republic of Korea
| | - Hong-Seok Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
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17
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António M, Lima T, Vitorino R, Daniel-da-Silva AL. Interaction of Colloidal Gold Nanoparticles with Urine and Saliva Biofluids: An Exploratory Study. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:4434. [PMID: 36558287 PMCID: PMC9785464 DOI: 10.3390/nano12244434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The use of gold nanoparticles for drug delivery, photothermal or photodynamic therapy, and biosensing enhances the demand for knowledge about the protein corona formed on the surface of nanoparticles. In this study, gold nanospheres (AuNSs), gold nanorods (AuNRs), and gold nanoflowers (AuNFs) were incubated with saliva or urine. After the interaction, the surface of gold nanoparticles was investigated using UV-VIS spectroscopy, zeta potential, and dynamic light scattering. The shifting of the localized surface plasmon resonance (LSPR) band, the increase in hydrodynamic diameter, and the changes in the surface charge of nanoparticles indicated the presence of biomolecules on the surface of AuNSs, AuNRs, and AuNFs. The incubation of AuNFs with saliva led to nanoparticle aggregation and minimal protein adsorption. AuNSs and AuNRs incubated in saliva were analyzed through liquid chromatography with tandem mass spectrometry (LC-MS/MS) to identify the 96 proteins adsorbed on the surface of the gold nanoparticles. Among the 20 most abundant proteins identified, 14 proteins were common in both AuNSs and AuNRs. We hypothesize that the adsorption of these proteins was due to their high sulfur content, allowing for their interaction with gold nanoparticles via the Au-S bond. The presence of distinct proteins on the surface of AuNSs or AuNRs was also investigated and possibly related to the competition between proteins present on the external layers of corona and gold nanoparticle morphology.
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Affiliation(s)
- Maria António
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Tânia Lima
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
| | - Rui Vitorino
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- UnIC@RISE, Department of Surgery and Phycology, Cardiovascular R&D Center, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Ana L. Daniel-da-Silva
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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18
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Wang MG, Wu SQ, Zhang MM, He JQ. Urine metabolomics and microbiome analyses reveal the mechanism of anti-tuberculosis drug-induced liver injury, as assessed for causality using the updated RUCAM: A prospective study. Front Immunol 2022; 13:1002126. [PMID: 36483548 PMCID: PMC9724621 DOI: 10.3389/fimmu.2022.1002126] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background Anti-tuberculosis drug-induced liver injury (ATB-DILI) is one of the most common adverse reactions that brings great difficulties to the treatment of tuberculosis. Thus, early identification of individuals at risk for ATB-DILI is urgent. We conducted a prospective cohort study to analyze the urinary metabolic and microbial profiles of patients with ATB-DILI before drug administration. And machine learning method was used to perform prediction model for ATB-DILI based on metabolomics, microbiome and clinical data. Methods A total of 74 new TB patients treated with standard first-line anti-TB treatment regimens were enrolled from West China Hospital of Sichuan University. Only patients with an updated RUCAM score of 6 or more were accepted in this study. Nontargeted metabolomics and microbiome analyses were performed on urine samples prior to anti-tuberculosis drug ingestion to screen the differential metabolites and microbes between the ATB-DILI group and the non-ATB-DILI group. Integrating electronic medical records, metabolomics, and microbiome data, four machine learning methods was used, including random forest algorithm, artificial neural network, support vector machine with the linear kernel and radial basis function kernel. Results Of all included patients, 69 patients completed follow-up, with 16 (23.19%) patients developing ATB-DILI after antituberculosis treatment. Finally, 14 ATB-DILI patients and 30 age- and sex-matched non-ATB-DILI patients were subjected to urinary metabolomic and microbiome analysis. A total of 28 major differential metabolites were screened out, involving bile secretion, nicotinate and nicotinamide metabolism, tryptophan metabolism, ABC transporters, etc. Negativicoccus and Actinotignum were upregulated in the ATB-DILI group. Multivariate analysis also showed significant metabolic and microbial differences between the non-ATB-DILI and severe ATB-DILI groups. Finally, the four models showed high accuracy in predicting ATB-DILI, with the area under the curve of more than 0.85 for the training set and 1 for the validation set. Conclusion This study characterized the metabolic and microbial profile of ATB-DILI risk individuals before drug ingestion for the first time. Metabolomic and microbiome characteristics in patient urine before anti-tuberculosis drug ingestion may predict the risk of liver injury after ingesting anti-tuberculosis drugs. Machine learning algorithms provides a new way to predict the occurrence of ATB-DILI among tuberculosis patients.
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Affiliation(s)
- Ming-Gui Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China,Department of Emergency Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Shou-Quan Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Meng-Meng Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jian-Qing He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Jian-Qing He, ;
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19
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Shansky Y, Bespyatykh J. Bile Acids: Physiological Activity and Perspectives of Using in Clinical and Laboratory Diagnostics. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227830. [PMID: 36431930 PMCID: PMC9692537 DOI: 10.3390/molecules27227830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Bile acids play a significant role in the digestion of nutrients. In addition, bile acids perform a signaling function through their blood-circulating fraction. They regulate the activity of nuclear and membrane receptors, located in many tissues. The gut microbiota is an important factor influencing the effects of bile acids via enzymatic modification. Depending on the rate of healthy and pathogenic microbiota, a number of bile acids may support lipid and glucose homeostasis as well as shift to more toxic compounds participating in many pathological conditions. Thus, bile acids can be possible biomarkers of human pathology. However, the chemical structure of bile acids is similar and their analysis requires sensitive and specific methods of analysis. In this review, we provide information on the chemical structure and the biosynthesis of bile acids, their regulation, and their physiological role. In addition, the review describes the involvement of bile acids in various diseases of the digestive system, the approaches and challenges in the analysis of bile acids, and the prospects of their use in omics technologies.
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Affiliation(s)
- Yaroslav Shansky
- Department of Molecular Medicine, Center of Molecular Medicine and Diagnostics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str., 1a, 119435 Moscow, Russia
- Correspondence:
| | - Julia Bespyatykh
- Department of Molecular Medicine, Center of Molecular Medicine and Diagnostics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str., 1a, 119435 Moscow, Russia
- Department of Expertise in Doping and Drug Control, Mendeleev University of Chemical Technology of Russia, Miusskaya Square, 9, 125047 Moscow, Russia
- Department of Public Health and Health Care, Federal Scientific State Budgetary Institution «N.A. Semashko National Research Institute of Public Health», Vorontsovo Pole Str., 12-1, 105064 Moscow, Russia
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Urinary Metabolomics Study on the Protective Role of Cocoa in Zucker Diabetic Rats via 1H-NMR-Based Approach. Nutrients 2022; 14:nu14194127. [PMID: 36235779 PMCID: PMC9572671 DOI: 10.3390/nu14194127] [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: 09/15/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022] Open
Abstract
Cocoa constitutes one of the richest sources of dietary flavonoids with demonstrated anti-diabetic potential. However, the metabolic impact of cocoa intake in a diabetic context remains unexplored. In this study, metabolomics tools have been used to investigate the potential metabolic changes induced by cocoa in type 2 diabetes (T2D). To this end, male Zucker diabetic fatty rats were fed on standard (ZDF) or 10% cocoa-rich diet (ZDF-C) from week 10 to 20 of life. Cocoa supplementation clearly decreased serum glucose levels, improved glucose metabolism and produced significant changes in the urine metabolome of ZDF animals. Fourteen differential urinary metabolites were identified, with eight of them significantly modified by cocoa. An analysis of pathways revealed that butanoate metabolism and the synthesis and degradation of branched-chain amino acids and ketone bodies are involved in the beneficial impact of cocoa on diabetes. Moreover, correlation analysis indicated major associations between some of these urine metabolites (mainly valine, leucine, and isoleucine) and body weight, glycemia, insulin sensitivity, and glycated hemoglobin levels. Overall, this untargeted metabolomics approach provides a clear metabolic fingerprint associated to chronic cocoa intake that can be used as a marker for the improvement of glucose homeostasis in a diabetic context.
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Shehzadi S, Khan SM, Mustafa G, Abdullah A, Khan I, Ahmad Z, Han H, Yu J, Park J, Raposo A. Antiviral COVID-19 protein and molecular docking: In silico characterization of various antiviral compounds extracted from Arisaema jacquemontii Blume. Front Public Health 2022; 10:964741. [PMID: 36211701 PMCID: PMC9540392 DOI: 10.3389/fpubh.2022.964741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/18/2022] [Indexed: 01/24/2023] Open
Abstract
Arisaema jacquemontii Blume is a highly medicinal and poisonous plant belong to the family Araceae. It is used to treat several deadly diseases, including viral infections. It has antioxidant, anti-cancerous, antimalarial, anti-vermicidal, and antiviral activities. Therefore, five parts of the Arisaema jacquemontii Blume plant, such as leaf, seed, stem, pulp, and rhizome extract, were evaluated for metabolic and in silico characterization of probable compounds using gas chromatography-mass spectrometry (GC-MS) analysis. A total of 22 compounds were isolated from the methanolic extracts of A. jacquemontii Blume. A selected antiviral COVID-19 protein i.e., protease (6LU7) was docked against the obtained compounds. Different affinities were obtained through various compounds. The best results were shown by three different compounds identified in the rhizome. The maximum binding affinity of these compounds is 8.1 kJ/mol. Molecular docking (MD) indicate that these molecules have the highest binding energies and hydrogen bonding interactions. The binding mode of interaction was discovered to be reasonably effective for counteracting the SARS virus COVID-19. The findings of this study could be extremely useful in the development of more phytochemical-based COVID-19 therapeutics.
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Affiliation(s)
- Sara Shehzadi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shujaul Mulk Khan
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan,Member, Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdullah Abdullah
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ilham Khan
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zeeshan Ahmad
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Heesup Han
- College of Hospitality and Tourism Management, Sejong University, Seoul, South Korea,*Correspondence: Heesup Han
| | - Jongsik Yu
- College of Business Division of Tourism and Hotel Management, Cheongju University, Cheongju-si, South Korea
| | - Junghyun Park
- College of Hospitality and Tourism Management, Sejong University, Seoul, South Korea
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal,António Raposo
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22
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Innovative Application of Metabolomics on Bioactive Ingredients of Foods. Foods 2022; 11:foods11192974. [PMID: 36230049 PMCID: PMC9562173 DOI: 10.3390/foods11192974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Metabolomics, as a new omics technology, has been widely accepted by researchers and has shown great potential in the field of nutrition and health in recent years. This review briefly introduces the process of metabolomics analysis, including sample preparation and extraction, derivatization, separation and detection, and data processing. This paper focuses on the application of metabolomics in food-derived bioactive ingredients. For example, metabolomics techniques are used to analyze metabolites in food to find bioactive substances or new metabolites in food materials. Moreover, bioactive substances have been tested in vitro and in vivo, as well as in humans, to investigate the changes of metabolites and the underlying metabolic pathways, among which metabolomics is used to find potential biomarkers and targets. Metabolomics provides a new approach for the prevention and regulation of chronic diseases and the study of the underlying mechanisms. It also provides strong support for the development of functional food or drugs. Although metabolomics has some limitations such as low sensitivity, poor repeatability, and limited detection range, it is developing rapidly in general, and also in the field of nutrition and health. At the end of this paper, we put forward our own insights on the development prospects of metabolomics in the application of bioactive ingredients in food.
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Xu W, Du J, Wei TT, Chen LY, Yang XX, Bo T, Liu HY, Xie MZ, Zhao TS, Yang JL, Cui F, Chen WW, Lu QB. Alterations in bile acids as metabolic signatures in the patients with human adenovirus type 7 infection. Front Med (Lausanne) 2022; 9:896409. [PMID: 36160124 PMCID: PMC9489940 DOI: 10.3389/fmed.2022.896409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives The changes in metabolism by human adenovirus (HAdV) infection was unclear. The potential mechanism of HAdV-7 causing acute respiratory tract infection was explored. Methods Totally 35 patients with HAdV-7 infection, 32 asymptomatic cases with HAdV-7 and 14 healthy controls were enrolled from an outbreak of HAdV-7 in the army. The serum samples were analyzed by untargeted and targeted metabolomics. The effects of differential metabolites were verified on HAdV-7 replication in an A549 cell line. Results The untargeted metabolomics analysis revealed more significant changes in the classes of sphingolipids, polyketides, glycerolipids, fatty acyls, and carboxylic acids and their derivatives in the patients with HAdV-7 than in healthy controls. Two key metabolic pathways of secondary and primary bile acid biosynthesis were noted from pathway enrichment analysis. Targeted metabolomics analysis showed that the levels of unconjugated bile acids in the patients were significantly lower, while the levels of glyco- and tauro- conjugated bile acids in patients and asymptomatic cases were higher than those in the healthy controls. The profiles of cytokines and peripheral lymphocyte subsets obviously varied at different levels of bile acids, with significant differences after HAdV-7 infection. A cell verification test demonstrated that the replication of HAdV-7 significantly reduced when GCDCA and TCA were added. Conclusion Bile acids inhibited HAdV-7 replication in vitro. Alterations in bile acids was metabolic signatures of HAdV-7 infected subjects, and our results suggested bile acids might play protective roles against HAdV-7 infection.
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Affiliation(s)
- Wen Xu
- Department of Infectious Disease, The Fifth Medical Center of Chinese People’s Liberation Army General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Juan Du
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
| | - Ting-Ting Wei
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
| | - Lin-Yi Chen
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
| | - Xin-Xin Yang
- Department of Infectious Disease, The Fifth Medical Center of Chinese People’s Liberation Army General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Tu Bo
- Department of Infectious Disease, The Fifth Medical Center of Chinese People’s Liberation Army General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Han-Yu Liu
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
| | - Ming-Zhu Xie
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
| | - Tian-Shuo Zhao
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
| | - Jun-Lian Yang
- Department of Infectious Disease, The Fifth Medical Center of Chinese People’s Liberation Army General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Fuqiang Cui
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
- *Correspondence: Fuqiang Cui,
| | - Wei-Wei Chen
- Department of Infectious Disease, The Fifth Medical Center of Chinese People’s Liberation Army General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
- Wei-Wei Chen,
| | - Qing-Bin Lu
- Department of Laboratorial Science and Technology and Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Global Center for Infectious Disease and Policy Research, Peking University, Beijing, China
- Qing-Bin Lu,
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António M, Lima T, Vitorino R, Daniel-da-Silva AL. Label-free dynamic light scattering assay for C-reactive protein detection using magnetic nanoparticles. Anal Chim Acta 2022; 1222:340169. [DOI: 10.1016/j.aca.2022.340169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022]
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A Metabolomic Approach and Traditional Physical Assessments to Compare U22 Soccer Players According to Their Competitive Level. BIOLOGY 2022; 11:biology11081103. [PMID: 35892959 PMCID: PMC9331507 DOI: 10.3390/biology11081103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
The purpose of this study was to use traditional physical assessments combined with a metabolomic approach to compare the anthropometric, physical fitness level, and serum fasting metabolic profile among U22 soccer players at different competitive levels. In the experimental design, two teams of male U22 soccer were evaluated (non-elite = 20 athletes, competing in a regional division; elite = 16 athletes, competing in the first division of the national U22 youth league). Earlobe blood samples were collected, and metabolites were extracted after overnight fasting (12 h). Untargeted metabolomics through Liquid Chromatograph Mass Spectrometry (LC-MS) analysis and anthropometric evaluation were performed. Critical velocity was applied to determine aerobic (CV) and anaerobic (ARC) capacity. Height (non-elite = 174.4 ± 7.0 cm; elite = 176.5 ± 7.0 cm), body mass index (non-elite = 22.1 ± 2.4 kg/m2; elite = 21.9 ± 2.3 kg/m2), body mass (non-elite = 67.1 ± 8.8 kg; elite = 68.5 ± 10.1 kg), lean body mass (non-elite = 59.3 ± 7.1 kg; elite = 61.1 ± 7.9 kg), body fat (non-elite = 7.8 ± 2.4 kg; elite = 7.3 ± 2.4 kg), body fat percentage (non-elite = 11.4 ± 2.4%; elite = 10.5 ± 1.7%), hematocrit (non-elite = 50.2 ± 4.0%; elite = 51.0 ± 4.0%), CV (non-elite = 3.1 ± 0.4 m/s; elite = 3.0 ± 0.2 m/s), and ARC (non-elite = 129.6 ± 55.7 m; elite = 161.5 ± 61.0 m) showed no significant differences between the elite and non-elite teams, while the multivariate Partial Least Squares Discriminant Analysis (PLS-DA) model revealed a separation between the elite and non-elite athletes. Nineteen metabolites with importance for projection (VIP) >1.0 were annotated as belonging to the glycerolipid, sterol lipid, fatty acyl, flavonoid, and glycerophospholipid classes. Metabolites with a high relative abundance in the elite group were related in the literature to a better level of aerobic power, greater efficiency in the recovery process, and improvement of mood, immunity, decision making, and accuracy, in addition to acting in mitochondrial preservation and electron transport chain maintenance. In conclusion, although classical physical assessments were not able to distinguish the teams at different competitive levels, the metabolomics approach successfully indicated differences between the fasting metabolic profiles of elite and non-elite teams.
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26
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Godage NH, Gionfriddo E. Biocompatible SPME coupled to GC/MS for analysis of xenobiotics in blood plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1203:123308. [DOI: 10.1016/j.jchromb.2022.123308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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27
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He XL, Hu XJ, Luo BY, Xia YY, Zhang T, Saffery R, De Seymour J, Zou Z, Xu G, Zhao X, Qi HB, Han TL, Zhang H, Baker PN. The effects of gestational diabetes mellitus with maternal age between 35 and 40 years on the metabolite profiles of plasma and urine. BMC Pregnancy Childbirth 2022; 22:174. [PMID: 35236326 PMCID: PMC8892719 DOI: 10.1186/s12884-022-04416-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 01/20/2022] [Indexed: 11/19/2022] Open
Abstract
Background Gestational diabetes mellitus (GDM) is defined as impaired glucose tolerance in pregnancy and without a history of diabetes mellitus. While there are limited metabolomic studies involving advanced maternal age in China, we aim to investigate the metabolomic profiling of plasma and urine in pregnancies complicated with GDM aged at 35–40 years at early and late gestation. Methods Twenty normal and 20 GDM pregnant participants (≥ 35 years old) were enlisted from the Complex Lipids in Mothers and Babies (CLIMB) study. Maternal plasma and urine collected at the first and third trimester were detected using gas chromatography-mass spectrometry (GC-MS). Results One hundred sixty-five metabolites and 192 metabolites were found in plasma and urine respectively. Urine metabolomic profiles were incapable to distinguish GDM from controls, in comparison, there were 14 and 39 significantly different plasma metabolites between the two groups in first and third trimester respectively. Especially, by integrating seven metabolites including cysteine, malonic acid, alanine, 11,14-eicosadienoic acid, stearic acid, arachidic acid, and 2-methyloctadecanoic acid using multivariant receiver operating characteristic models, we were capable of discriminating GDM from normal pregnancies with an area under curve of 0.928 at first trimester. Conclusion This study explores metabolomic profiles between GDM and normal pregnancies at the age of 35–40 years longitudinally. Several compounds have the potential to be biomarkers to predict GDM with advanced maternal age. Moreover, the discordant metabolome profiles between the two groups could be useful to understand the etiology of GDM with advanced maternal age. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-022-04416-5.
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Affiliation(s)
- Xiao-Ling He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China.,State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016, China
| | - Xiao-Jing Hu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Bai-Yu Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Yin-Yin Xia
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
| | - Ting Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China.,State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016, China
| | - Richard Saffery
- Cancer & Disease Epigenetics, Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | | | - Zhen Zou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Ge Xu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Xue Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Hong-Bo Qi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China.,State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016, China
| | - Ting-Li Han
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China. .,State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016, China. .,Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China. .,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Hua Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China. .,State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016, China.
| | - Philip N Baker
- College of Life Sciences, University of Leicester, Leicester, UK
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Kushak RI, Sengupta A, Winter HS. Interactions between the intestinal microbiota and epigenome in individuals with autism spectrum disorder. Dev Med Child Neurol 2022; 64:296-304. [PMID: 34523735 DOI: 10.1111/dmcn.15052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/27/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by variable impairment of cognitive function and interpersonal relationships. Furthermore, some individuals with ASD have gastrointestinal disorders that have been correlated with impairments in intestinal microbiota. Gut microbiota are important not only for intestinal health, but also for many other functions including food digestion, energy production, immune system regulation, and, according to current data, behavior. Disruption of the indigenous microbiota, microbial dysbiosis (imbalance between microorganisms present in the gut), overgrowth of potentially pathogenic microorganisms, a less diverse microbiome, or lower levels of beneficial bacteria in children with ASD can affect behavior. Metabolome analysis in children with ASD has identified perturbations in multiple metabolic pathways that might be associated with cognitive functions. Recent studies have shown that the intestinal microbiome provides environmental signals that can modify host response to stimuli by modifying the host epigenome, which affects DNA methylation, histone modification, and non-coding RNAs. The most studied microbiota-produced epigenetic modifiers are short-chain fatty acids, although other products of intestinal microbiota might also cause epigenetic modifications in the host's DNA. Here we review evidence suggesting that epigenetic alterations caused by modification of gene expression play an important role in understanding ASD.
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Affiliation(s)
- Rafail I Kushak
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ashok Sengupta
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Harland S Winter
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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29
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Boullaud L, Blasco H, Trinh TT, Bakhos D. Metabolomic Studies in Inner Ear Pathologies. Metabolites 2022; 12:metabo12030214. [PMID: 35323657 PMCID: PMC8955628 DOI: 10.3390/metabo12030214] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022] Open
Abstract
Sensorineural hearing loss is the most common sensory deficit. The etiologies of sensorineural hearing loss have been described and can be congenital or acquired. For congenital non-syndromic hearing loss, mutations that are related to sites of cochlear damage have been discovered (e.g., connexin proteins, mitochondrial genes, etc.). For cytomegalovirus infection or auditory neuropathies, mechanisms are also well known and well researched. Although the etiologies of sensorineural hearing loss may be evident for some patients, the damaged sites and pathological mechanisms remain unclear for patients with progressive post-lingual hearing loss. Metabolomics is an emerging technique in which all metabolites present in a sample at a given time are analyzed, reflecting a physiological state. The objective of this study was to review the literature on the use of metabolomics in hearing loss. The findings of this review suggest that metabolomic studies may help to develop objective tests for diagnosis and personalized treatment.
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Affiliation(s)
- Luc Boullaud
- ENT Department and Cervico-Facial Surgery, University Center Hospital of Tours, 2 Boulevard Tonnellé, 37044 Tours, France; (T.-T.T.); (D.B.)
- INSERM U1253, iBrain, University of Tours, 10 Boulevard Tonnellé, 37000 Tours, France;
- Correspondence: ; Tel.: +33-247-474-785; Fax: +33-247-473-600
| | - Hélène Blasco
- INSERM U1253, iBrain, University of Tours, 10 Boulevard Tonnellé, 37000 Tours, France;
- Faculty of Medicine, University of Tours, 10 Boulevard Tonnellé, 37000 Tours, France
- Department of Biochemistry and Molecular Biology, University Center Hospital of Tours, 2 Boulevard Tonnellé, 37044 Tours, France
| | - Thuy-Trân Trinh
- ENT Department and Cervico-Facial Surgery, University Center Hospital of Tours, 2 Boulevard Tonnellé, 37044 Tours, France; (T.-T.T.); (D.B.)
- Faculty of Medicine, University of Tours, 10 Boulevard Tonnellé, 37000 Tours, France
| | - David Bakhos
- ENT Department and Cervico-Facial Surgery, University Center Hospital of Tours, 2 Boulevard Tonnellé, 37044 Tours, France; (T.-T.T.); (D.B.)
- INSERM U1253, iBrain, University of Tours, 10 Boulevard Tonnellé, 37000 Tours, France;
- Faculty of Medicine, University of Tours, 10 Boulevard Tonnellé, 37000 Tours, France
- House Institute Foundation, Los Angeles, CA 90057, USA
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30
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Kondoh H, Teruya T, Kameda M, Yanagida M. Decline of ergothioneine in frailty and cognition impairment. FEBS Lett 2022; 596:1270-1278. [PMID: 35090053 DOI: 10.1002/1873-3468.14299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/08/2022]
Abstract
Ergothioneine is a well-known anti-oxidant that is abundant in both human red blood cells and in fission yeast responding to nutritional stress. In frail elderly people, whose aging organs undergo functional decline, there is a correlation between ergothioneine levels and cognitive, but not skeletal muscle decline. In patients suffering from dementia, including Alzheimer's disease with hippocampal atrophy, deteriorating cognitive ability is correlated with declining ergothioneine levels. S-methyl-ergothioneine, trimethyl-histidine, and three other trimethyl-ammonium compounds also decrease sharply in dementia, whereas compounds such as indoxyl-sulfate and quinolinic acid increase, possibly exacerbating the disease. Using these opposing dementia markers, not only diagnosis, but also therapeutic interventions to mitigate cognitive decline may now become possible.
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Affiliation(s)
- Hiroshi Kondoh
- Geriatric unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Teruya
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Masahiro Kameda
- Geriatric unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
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Metabolomics profiling of human exhaled breath condensate by SPME/GC × GC-ToFMS: Exploratory study on the use of face masks at the level of lipid peroxidation volatile markers. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Liu S, You Y, Tong Z, Zhang L. Developing an Embedding, Koopman and Autoencoder Technologies-Based Multi-Omics Time Series Predictive Model (EKATP) for Systems Biology research. Front Genet 2021; 12:761629. [PMID: 34764986 PMCID: PMC8576451 DOI: 10.3389/fgene.2021.761629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
It is very important for systems biologists to predict the state of the multi-omics time series for disease occurrence and health detection. However, it is difficult to make the prediction due to the high-dimensional, nonlinear and noisy characteristics of the multi-omics time series data. For this reason, this study innovatively proposes an Embedding, Koopman and Autoencoder technologies-based multi-omics time series predictive model (EKATP) to predict the future state of a high-dimensional nonlinear multi-omics time series. We evaluate this EKATP by using a genomics time series with chaotic behavior, a proteomics time series with oscillating behavior and a metabolomics time series with flow behavior. The computational experiments demonstrate that our proposed EKATP can substantially improve the accuracy, robustness and generalizability to predict the future state of a time series for multi-omics data.
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Affiliation(s)
- Suran Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Yujie You
- College of Computer Science, Sichuan University, Chengdu, China
| | - Zhaoqi Tong
- College of Software Engineering, Sichuan University, Chengdu, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu, China
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Cui D, Li W, Jiang D, Wu J, Xie J, Wu Y. Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma. Front Med (Lausanne) 2021; 8:754709. [PMID: 34660653 PMCID: PMC8514776 DOI: 10.3389/fmed.2021.754709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) specifically infects liver cells, leading to progressive liver cirrhosis and significantly increasing the risk of hepatocellular carcinoma (HCC). The maturity of sequencing technology, improvement in bioinformatics data analysis and progress of omics technologies had improved research efficiency. The occurrence and progression of HCC are affected by multisystem and multilevel pathological changes. With the application of single-omics technologies, including genomics, transcriptomics, metabolomics and proteomics in tissue and body fluid samples, and even the novel development of multi-omics analysis on a single-cell platform, HBV-associated HCC changes can be better analyzed. The review summarizes the application of single omics and combined analysis of multi-omics data in HBV-associated HCC and proposes the importance of multi-omics analysis in the type of HCC, which provide the possibility for the precise diagnosis and therapy of HBV-associated HCC.
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Affiliation(s)
- Dawei Cui
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Li
- Center of Research Laboratory, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Daixi Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianguo Wu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Jue Xie
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
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Nannini G, Meoni G, Tenori L, Ringressi MN, Taddei A, Niccolai E, Baldi S, Russo E, Luchinat C, Amedei A. Fecal metabolomic profiles: A comparative study of patients with colorectal cancer vs adenomatous polyps. World J Gastroenterol 2021; 27:6430-6441. [PMID: 34720532 PMCID: PMC8517777 DOI: 10.3748/wjg.v27.i38.6430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/17/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC), the third most common cause of death in both males and females worldwide, shows a positive response to therapy and usually a better prognosis when detected at an early stage. However, the survival rate declines when the diagnosis is late and the tumor spreads to other organs. Currently, the measures widely used in the clinic are fecal occult blood test and evaluation of serum tumor markers, but the lack of sensitivity and specificity of these markers restricts their use for CRC diagnosis. Due to its high sensitivity and precision, colonoscopy is currently the gold-standard screening technique for CRC, but it is a costly and invasive procedure. Therefore, the implementation of custom-made methodologies including those with minimal invasiveness, protection, and reproducibility is highly desirable. With regard to other screening methods, the screening of fecal samples has several benefits, and metabolomics is a successful method to classify the metabolite shift in living systems as a reaction to pathophysiological influences, genetic modifications, and environmental factors.
AIM To characterize the variation groups and potentially recognize some diagnostic markers, we compared with healthy controls (HCs) the fecal nuclear magnetic resonance (NMR) metabolomic profiles of patients with CRC or adenomatous polyposis (AP).
METHODS Proton nuclear magnetic resonance spectroscopy was used in combination with multivariate and univariate statistical approaches, to define the fecal metabolic profiles of 32 CRC patients, 16 AP patients, and 38 HCs well matched in age, sex, and body mass index.
RESULTS NMR metabolomic analyses revealed that fecal sample profiles differed among CRC patients, AP patients, and HCs, and some discriminatory metabolites including acetate, butyrate, propionate, 3-hydroxyphenylacetic acid, valine, tyrosine and leucine were identified.
CONCLUSION In conclusion, we are confident that our data can be a forerunner for future studies on CRC management, especially the diagnosis and evaluation of the effectiveness of treatments.
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Affiliation(s)
- Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gaia Meoni
- Department of Chemistry “Ugo Schiff”, University of Florence, Florence 50134, Italy
| | - Leonardo Tenori
- Department of Chemistry “Ugo Schiff”, University of Florence, Florence 50134, Italy
| | - Maria Novella Ringressi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Antonio Taddei
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Elena Niccolai
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Simone Baldi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Claudio Luchinat
- Department of Chemistry & Magnetic Resonance Center (CERM), University of Florence, Florence 50134, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
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Araújo AM, Carvalho F, Guedes de Pinho P, Carvalho M. Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions. Metabolites 2021; 11:692. [PMID: 34677407 PMCID: PMC8539642 DOI: 10.3390/metabo11100692] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
Given the high biological impact of classical and emerging toxicants, a sensitive and comprehensive assessment of the hazards and risks of these substances to organisms is urgently needed. In this sense, toxicometabolomics emerged as a new and growing field in life sciences, which use metabolomics to provide new sets of susceptibility, exposure, and/or effects biomarkers; and to characterize in detail the metabolic responses and altered biological pathways that various stressful stimuli cause in many organisms. The present review focuses on the analytical platforms and the typical workflow employed in toxicometabolomic studies, and gives an overview of recent exploratory research that applied metabolomics in various areas of toxicology.
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Affiliation(s)
- Ana Margarida Araújo
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Félix Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Márcia Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
- FP-I3ID, FP-ENAS, University Fernando Pessoa, Praça 9 de Abril, 349, 4249-004 Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150 Porto, Portugal
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Salivary metabolomics – A diagnostic and biologic signature for oral cancer. JOURNAL OF ORAL AND MAXILLOFACIAL SURGERY, MEDICINE, AND PATHOLOGY 2021. [DOI: 10.1016/j.ajoms.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Identification of potential serum metabolic biomarkers for patient with keratoconus using untargeted metabolomics approach. Exp Eye Res 2021; 211:108734. [PMID: 34428458 DOI: 10.1016/j.exer.2021.108734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/01/2021] [Accepted: 08/17/2021] [Indexed: 11/22/2022]
Abstract
This study aimed to investigate the metabolite differences between patients with keratoconus and control subjects and identify potential serum biomarkers for keratoconus using a non-targeted metabolomics approach. Venous blood samples were obtained from patients with keratoconus (n = 20) as well as from age-, gender- and race-matched control subjects (n = 20). Metabolites extracted from serum were separated and analyzed by liquid chromatography/quadrupole time-of-flight mass spectrometer. Processing of raw data and analysis of the data files was performed using Agilent Mass Hunter Qualitative software. The identified metabolites were subjected to a principal component and hierarchical cluster analysis. Appropriate statistical tests were used to analyze the metabolomic profiling data. Together, the analysis revealed that the dehydroepiandrosterone sulfate from the steroidal hormone synthesis pathway was significantly upregulated in patients with keratoconus (p < 0.05). Also, a combination of eicosanoids from the arachidonic acid pathway, mainly prostaglandin F2α, prostaglandin A2, 16,16-dimethyl prostaglandin E2, and 5-hydroxyeicosatetraenoic acid were collectively up-regulated as a group in keratoconus patients (p < 0.05). On the other hand, glycerophospholipid PS(17:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)) was found to be significantly upregulated in the metabolomics profiles of control subjects (p < 0.05). The differently regulated metabolites provide insights into the pathophysiology of keratoconus and could potentially be used as biomarkers for keratoconus to aid in screening for individuals at risk hence, enabling early diagnosis and timely monitoring of disease.
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Barzaghi S, Monti L, Marinoni L, Cattaneo TMP. Chemometrics for the Identification of Nitrogen and Acid Compounds in Milk-Whey as By-Products from Crescenza and Grana Padano Type Cheese-Making. Molecules 2021; 26:molecules26164839. [PMID: 34443426 PMCID: PMC8398050 DOI: 10.3390/molecules26164839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/28/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022] Open
Abstract
Proteomics and metabolomics are analytic tools used in combination with bioinformatics to study proteins and metabolites which contribute to describing complex biological systems. The growing interest in research concerning the resolution of these systems has stimulated the development of sophisticated procedures and new applications. This paper introduces the evolution of statistical techniques for the treatment of data, suggesting the possibility to successfully characterize the milk-whey syneresis process by applying two-dimensional correlation analysis (2DCOR) to a series of CE electropherograms referring to milk-whey samples collected during cheese manufacturing. Two cheese-making processes to produce hard cheese (Grana type) and fresh cheese (Crescenza) were taken as models. The applied chemometric tools were shown to be useful for the treatment of data acquired in a systematically perturbed chemical system as a function of time.
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Affiliation(s)
- Stefania Barzaghi
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics, Via A. Lombardo, 11, 26900 Lodi, Italy;
- Correspondence: ; Tel.: +39-0371-4501262
| | - Lucia Monti
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics, Via A. Lombardo, 11, 26900 Lodi, Italy;
| | - Laura Marinoni
- Research Centre for Engineering and Agro-Food Processing, Council for Agricultural Research and Economics, Via G. Venezian, 26, 20133 Milano, Italy; (L.M.); (T.M.P.C.)
| | - Tiziana M. P. Cattaneo
- Research Centre for Engineering and Agro-Food Processing, Council for Agricultural Research and Economics, Via G. Venezian, 26, 20133 Milano, Italy; (L.M.); (T.M.P.C.)
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GC-MS Based Metabolomics Reveals the Synergistic Mechanism of Gardeniae Fructus-Forsythiae Fructus Herb Pair in Lipopolysaccharide-Induced Acute Lung Injury Mouse Model. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:8064557. [PMID: 34354760 PMCID: PMC8331283 DOI: 10.1155/2021/8064557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/17/2021] [Indexed: 11/18/2022]
Abstract
Compatibility remains among the crucial and significant characteristics of traditional Chinese medicines. The Gardeniae Fructus (FG)-Forsythiae Fructus (FF) herb pair, an epitome of formulations for heat-clearing and detoxification, is extensively used to treat bacterial pneumonia in clinical settings. However, there are few reports on their synergistic effects. This study thus investigated their compatibility by GC-MS based metabolomics using a lipopolysaccharide (LPS)-induced acute lung injury (ALI) mouse model. Differential metabolites were identified by both variable importance in the projection (VIP) > 1 in orthogonal partial least-squares discriminant analysis (OPLS-DA) mode and P < 0.05. Results of biochemistry and histopathology indicated that FG-FF herb pair exerted more promising lung protective effect than its individual decoction against the LPS-induced ALI model. From the metabolomics study, 32 differential metabolites in vehicle vs. model groups, 21 differential metabolites in FF vs. model groups, 21 differential metabolites in FG vs. model groups, and 20 differential metabolites in FG-FF herb pair vs. model groups were found. Among them, the levels of 3-hydroxybutyric acid, alanine, isophthalic acid, and terephthalic acid were restored significantly in the FF group, while silanol and cholesterol were restored significantly in the FG group. For FG-FF treatment, the amount of behenic acid, a metabolite with anti-inflammatory properties, was increased, while palmitic acid, a proinflammatory metabolite, was decreased. Meanwhile, the two biomarkers were restored more significantly than that by FG or FF treatment, which indicated that the synergistic effects by FF coupled with FG might be attributed to restoring fatty acids metabolic pathway.
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40
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Sun R, Cui C, Zhou Y, Cui Q. Comprehensive Analysis of RNA Expression Correlations between Biofluids and Human Tissues. Genes (Basel) 2021; 12:935. [PMID: 34207420 PMCID: PMC8234006 DOI: 10.3390/genes12060935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
In recent years, biofluid has been considered a promising source of non-invasive biomarkers for health monitoring and disease diagnosis. However, the expression consistency between biofluid and human tissue, which is fundamental to RNA biomarker development, has not been fully evaluated. In this study, we collected expression profiles across 53 human tissues and five main biofluid types. Utilizing the above dataset, we uncovered a globally positive correlation pattern between various biofluids (including blood, urine, bile, saliva and stool) and human tissues. However, significantly varied biofluid-tissue similarity levels and tendencies were observed between mRNA and lncRNA. Moreover, a higher correlation was found between biofluid types and their functionally related and anatomically closer tissues. In particular, a highly specific correlation was discovered between urine and the prostate. The biological sex of the donor was also proved to be an important influencing factor in biofluid-tissue correlation. Moreover, genes enriched in basic biological processes were found to display low variability across biofluid types, while genes enriched in catabolism-associated pathways were identified as highly variable.
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Affiliation(s)
| | | | | | - Qinghua Cui
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Center for Non-Coding RNA Medicine, Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (R.S.); (C.C.); (Y.Z.)
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Zhang F, Wang Y, Chen G, Li Z, Xing X, Putz-Bankuti C, Stauber RE, Liu X, Madl T. Growing Human Hepatocellular Tumors Undergo a Global Metabolic Reprogramming. Cancers (Basel) 2021; 13:1980. [PMID: 33924061 PMCID: PMC8074141 DOI: 10.3390/cancers13081980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy with poor prognosis, high morbidity and mortality concerning with lack of effective diagnosis and high postoperative recurrence. Similar with other cancers, HCC cancer cells have to alter their metabolism to adapt to the changing requirements imposed by the environment of the growing tumor. In less vascularized regions of tumor, cancer cells experience hypoxia and nutrient starvation. Here, we show that HCC undergoes a global metabolic reprogramming during tumor growth. A combined proteomics and metabolomics analysis of paired peritumoral and tumor tissues from 200 HCC patients revealed liver-specific metabolic reprogramming and metabolic alterations with increasing tumor sizes. Several proteins and metabolites associated with glycolysis, the tricarboxylic acid cycle and pyrimidine synthesis were found to be differentially regulated in serum, tumor and peritumoral tissue with increased tumor sizes. Several prognostic metabolite biomarkers involved in HCC metabolic reprogramming were identified and integrated with clinical and pathological data. We built and validated this combined model to discriminate against patients with different recurrence risks. An integrated and comprehensive metabolomic analysis of HCC is provided by our present work. Metabolomic alterations associated with the advanced stage of the disease and poor clinical outcomes, were revealed. Targeting cancer metabolism may deliver effective therapies for HCC.
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Affiliation(s)
- Fangrong Zhang
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria;
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Csilla Putz-Bankuti
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (C.P.-B.); (R.E.S.)
| | - Rudolf E. Stauber
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (C.P.-B.); (R.E.S.)
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
- Xiamen Institute of Rare Earth Materials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Xiamen 361024, China
| | - Tobias Madl
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria;
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
- Xiamen Institute of Rare Earth Materials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Xiamen 361024, China
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António M, Vitorino R, Daniel-da-Silva AL. Gold nanoparticles-based assays for biodetection in urine. Talanta 2021; 230:122345. [PMID: 33934794 DOI: 10.1016/j.talanta.2021.122345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Urine is a biofluid easy to collect through a non-invasive technique that allows collecting a large volume of sample. The use of urine for disease diagnosis is not yet well explored. However, it has gained attention over the last three years. It has been applied in the diagnosis of several illnesses such as kidney disease, bladder cancer, prostate cancer and cardiovascular diseases. In the last decade, gold nanoparticles (Au NPs) have attracted attention in biosensors' development for the diagnosis of diseases due to their electrical and optical properties, ability to conjugate with biomolecules, high sensitivity, and selectivity. Therefore, this article aims to present a comprehensive view of state of the art on the advances made in the quantification of analytes in urinary samples using AuNPs based assays, with a focus on protein analysis. The type of diagnosis methods, the Au NPs synthesis approaches and the strategies for surface modification aiming at selectivity towards the different targets are highlighted.
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Affiliation(s)
- Maria António
- CICECO-Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Rui Vitorino
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal; Department of Surgery and Physiology, Cardiovascular R&D Center, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal; LAQV-REQUIMTE, Chemistry Department, University of Aveiro, Aveiro, Portugal.
| | - Ana L Daniel-da-Silva
- CICECO-Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193, Aveiro, Portugal.
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Mikhail IE, Tehranirokh M, Gooley AA, Guijt RM, Breadmore MC. Hyphenated sample preparation-electrospray and nano-electrospray ionization mass spectrometry for biofluid analysis. J Chromatogr A 2021; 1646:462086. [PMID: 33892255 DOI: 10.1016/j.chroma.2021.462086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Stand-alone electrospray ionization mass spectrometry (ESI-MS) has been advancing through enhancements in throughput, selectivity and sensitivity of mass spectrometers. Unlike traditional MS techniques which usually require extensive offline sample preparation and chromatographic separation, many sample preparation techniques are now directly coupled with stand-alone MS to enable outstanding throughput for bioanalysis. In this review, we summarize the different sample clean-up and/or analyte enrichment strategies that can be directly coupled with ESI-MS and nano-ESI-MS for the analysis of biological fluids. The overview covers the hyphenation of different sample preparation techniques including solid phase extraction (SPE), solid phase micro-extraction (SPME), slug flow micro-extraction/nano-extraction (SFME/SFNE), liquid extraction surface analysis (LESA), extraction electrospray, extraction using digital microfluidics (DMF), and electrokinetic extraction (EkE) with ESI-MS and nano-ESI-MS.
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Affiliation(s)
- Ibraam E Mikhail
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech), Australia; Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, Tasmania 7001, Australia; Department of Analytical Chemistry, Faculty of Pharmacy, Mansoura University, 35516, Egypt
| | - Masoomeh Tehranirokh
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech), Australia; Trajan Scientific and Medical, Ringwood, VIC, 3134, Australia
| | - Andrew A Gooley
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech), Australia; Trajan Scientific and Medical, Ringwood, VIC, 3134, Australia
| | - Rosanne M Guijt
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech), Australia; Centre for Regional and Rural Futures, Deakin University, Geelong, VIC, 3220, Australia
| | - Michael C Breadmore
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech), Australia; Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, Tasmania 7001, Australia.
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Kuang J, Xu P, Shi Y, Yang Y, Liu P, Chen S, Zhou C, Li G, Zhuang Y, Hu R, Hu G, Guo X. Nephropathogenic Infectious Bronchitis Virus Infection Altered the Metabolome Profile and Immune Function of the Bursa of Fabricius in Chicken. Front Vet Sci 2021; 7:628270. [PMID: 33553290 PMCID: PMC7858655 DOI: 10.3389/fvets.2020.628270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/15/2020] [Indexed: 01/22/2023] Open
Abstract
Infectious bronchitis is a highly contagious, acute viral respiratory disease of chickens, regardless of the strain, and its infection may lead to considerable economic losses to the poultry industry. New nephropathogenic infectious bronchitis virus (NIBV) strains have increasingly emerged in recent years; hence, evaluating their infection-influenced immune function changes and the alteration of metabolite profiling is important. Initially, chickens were randomly distributed into two groups: the control group (Con) and the disease group (Dis). Here, the partial cytokines were examined, and the metabolome alterations of the bursa of Fabricius (BF) in NIBV infections in chickens were profiled by gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). The results revealed that the NIBV infection promotes the mRNA expression of inflammatory cytokines. Metabolic profile analysis indicated that clustering differed between the two groups and there were 75 significantly different metabolites detected between the two groups, suggesting that the host metabolism was significantly changed by NIBV infection. Notably, the following 12 metabolites were identified as the potential biomarkers: 3-phenyllactic acid, 2-deoxytetronic acid, aminomalonic acid, malonamide 5, uric acid, arachidonic acid, 2-methylglutaric acid, linoleic acid, ethanolamine, stearic acid, N-alpha-acetyl-l-ornithine, and O-acetylserine. Furthermore, the results of the correlation analysis showed that a strong correlation existed between metabolic biomarkers and inflammatory cytokines. Our results describe an immune and metabolic profile for the BF of chickens when infected with NIBV and provide new biomarkers of NIBV infection as potential targets and indicators of indicating therapeutic efficacy.
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Affiliation(s)
- Jun Kuang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Puzhi Xu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yan Shi
- School of Computer and Information Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yitian Yang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shupeng Chen
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Changming Zhou
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Guyue Li
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yu Zhuang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ruiming Hu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
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Reyes-Garcés N, Boyacı E, Gómez-Ríos GA, Olkowicz M, Monnin C, Bojko B, Vuckovic D, Pawliszyn J. Assessment of solid phase microextraction as a sample preparation tool for untargeted analysis of brain tissue using liquid chromatography-mass spectrometry. J Chromatogr A 2021; 1638:461862. [PMID: 33433374 DOI: 10.1016/j.chroma.2020.461862] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/19/2020] [Accepted: 12/25/2020] [Indexed: 12/14/2022]
Abstract
This work presents an evaluation of solid-phase microextraction (SPME) SPME in combination with liquid chromatography-high resolution mass spectrometry (LC-HRMS) as an analytical approach for untargeted brain analysis. The study included a characterization of the metabolite coverage provided by C18, mixed-mode (MM, with benzene sulfonic acid and C18 functionalities), and hydrophilic lipophilic balanced (HLB) particles as sorbents in SPME coatings after extraction from cow brain homogenate at static conditions. The effects of desorption solvent, extraction time, and chromatographic modes on the metabolite features detected were investigated. Method precision and absolute matrix effects were also assessed. Among the main findings of this work, it was observed that all three tested coating chemistries were able to provide comparable brain tissue information. HLB provided higher responses for polar metabolites; however, as these fibers were prepared in-house, higher inter-fiber relative standard deviations were also observed. C18 and HLB coatings offered similar responses with respect to lipid-related features, whereas MM and C18 provided the best results in terms of method precision. Our results also showed that the use of methanol is essential for effective desorption of non-polar metabolites. Using a reversed-phase chromatographic method, an average of 800 and 1200 brain metabolite features detected in positive and negative modes, respectively, met inter-fibre RSD values below 30% (n=4) after removal of fibre and solvent artefacts from the associated datasets. For features detected using a lipidomics method, a total of 900 and 1800 features detected using C18 fibers in positive and negative mode, respectively, met the same criteria. In terms of absolute matrix effects, the majority of the model metabolites tested showed values between 80 and 120%, which are within the acceptable range. Overall, the findings of this work lay the foundation for further optimization of parameters for SPME-LC-HRMS methods suitable for in vivo and ex vivo brain (and other tissue) untargeted studies, and support the applicability of this approach for non-destructive tissue metabolomics.
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Affiliation(s)
| | - Ezel Boyacı
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada
| | | | - Mariola Olkowicz
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada
| | - Cian Monnin
- Department of Chemistry and Biochemistry, Concordia University, Montreal QC H4B 1R6, Canada
| | - Barbara Bojko
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada
| | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montreal QC H4B 1R6, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada.
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Metabolic Changes in Serum Metabolome of Beagle Dogs Fed Black Ginseng. Metabolites 2020; 10:metabo10120517. [PMID: 33352805 PMCID: PMC7765939 DOI: 10.3390/metabo10120517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022] Open
Abstract
The effects of black ginseng, which has many kinds of biological activities, on dogs was investigated. Serum samples of beagle dogs, which were fed with black ginseng for 8 weeks, were measured using high-resolution magic angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectrometry. Acquired NMR data from the serum of dogs fed for 0, 4, and 8 weeks were analyzed by metabolic profiling and multivariate statistical analysis. In statistical analysis and biomarker analysis results of metabolite profiles, formate, glutamine, histidine, isoleucine, leucine, proline, and valine had variable importance in projection (VIP) scores above 1.0 and excellent area under the curve (AUC) values of receiver operating characteristic (ROC) curves above 0.9. In the result of multivariate statistical analysis, the score plot showed the discrimination between before and after feeding of black ginseng. These differences in metabolic profiles are considered to be due to the involvement of metabolic processes following black ginseng administration, such as enhancing immunity and energy metabolism. Through metabolomics analysis, we confirmed the biological efficacy of black ginseng in dogs and also confirmed that metabolomics can be applied to the pet health industry.
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Liang Y, Xiao Z, Ke X, Yao P, Chen Y, Lin L, Lu J. Urinary Metabonomic Profiling Discriminates Between Children with Autism and Their Healthy Siblings. Med Sci Monit 2020; 26:e926634. [PMID: 33237888 PMCID: PMC7702663 DOI: 10.12659/msm.926634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a complicated neuropsychiatric disease that displays significant heterogeneity. The diagnosis of ASD is currently primarily dependent upon descriptions of clinical symptoms, and it remains urgent to find biological markers for the detection and diagnosis of autism. The current study applied the urinary metabolic profiling approach to characterize metabolic phenotypes in ASD. Material/Methods Urine was obtained from children with ASD and their matched healthy siblings. Samples were analyzed using 1H NMR-based methods designed to measure a broad range of metabolites. Partial least-square-discriminant analysis (PLS-DA) was used to develop models to identify metabonomic variations that can be used to distinguish between individuals with ASD and their unaffected siblings. Results A significant difference was observed between the metabolomic profiles of children with ASD and that of their healthy siblings. An increase in the levels of tryptophan, hippurate, glycine, and creatine, and a decrease in trigonelline, melatonin, pantothenate, serotonin, and taurine were observed compared to the control group. We conclude that several metabolic pathways are affected by autism, which suggests that a gut-brain link may be important in the pathophysiology of ASD. Conclusions 1H NMR-based metabonomic analysis of the urine can determine perturbations of specific metabolic pathways related to ASD and help identify a characteristic metabolic fingerprint to better understand the disease and its causes.
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Affiliation(s)
- Yujie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland).,Faculty of Mental health, Shenzhen University, Shenzhen, Guangdong, China (mainland)
| | - Zhou Xiao
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland)
| | - Xiaoyin Ke
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland)
| | - Paul Yao
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland)
| | - Yangxia Chen
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland)
| | - Ling Lin
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland).,Faculty of Mental health, Shenzhen University, Shenzhen, Guangdong, China (mainland)
| | - Jianping Lu
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental Health, Shenzhen, Guangdong, China (mainland).,Faculty of Mental health, Shenzhen University, Shenzhen, Guangdong, China (mainland)
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Alberti P. A review of novel biomarkers and imaging techniques for assessing the severity of chemotherapy-induced peripheral neuropathy. Expert Opin Drug Metab Toxicol 2020; 16:1147-1158. [DOI: 10.1080/17425255.2021.1842873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Paola Alberti
- Experimental Neurology Unit, School of Medicine and Surgery, Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy and NeuroMI (Milan Center for Neuroscience), Milan, Italy
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Valko-Rokytovská M, Očenáš P, Salayová A, Titková R, Kostecká Z. Specific urinary metabolites in canine mammary gland tumors. J Vet Sci 2020; 21:e23. [PMID: 32233131 PMCID: PMC7113568 DOI: 10.4142/jvs.2020.21.e23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 12/12/2022] Open
Abstract
The identification of biomarkers that distinguish diseased from healthy individuals is of great interest in human and veterinary fields. In this research area, a metabolomic approach and its related statistical analyses can be useful for biomarker determination and allow non-invasive discrimination of healthy volunteers from breast cancer patients. In this study, we focused on the most common canine neoplasm, mammary gland tumor, and herein, we describe a simple method using ultra-high-performance liquid chromatography to determine the levels of tyrosine and its metabolites (epinephrine, 3,4-dihydroxy-L-phenylalanine, 3,4-dihydroxyphenylacetic acid, and vanillylmandelic acid), tryptophan and its metabolites (5-hydroxyindolacetic acid, indoxyl sulfate, serotonin, and kynurenic acid) in canine mammary cancer urine samples. Our results indicated significantly increased concentrations of three tryptophan metabolites, 5-hydroxyindolacetic acid (p < 0.001), serotonin, indoxyl sulfate (p < 0.01), and kynurenic acid (p < 0.05), and 2 tyrosine metabolites, 3,4-dihydroxy-L-phenylalanine (p < 0.001), and epinephrine (p < 0.05) in urine samples from the mammary gland tumor group compared to concentrations in urine samples from the healthy group. The results indicate that select urinary tyrosine and tryptophan metabolites may be useful as non-invasive diagnostic markers as well as in developing a therapeutic strategy for canine mammary gland tumors.
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Affiliation(s)
- Marcela Valko-Rokytovská
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia.
| | - Peter Očenáš
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia.
| | - Aneta Salayová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia.
| | - Radka Titková
- Section of Surgery, Orthopaedics, Roentgenology and Reproduction, Small Animal Clinic, University Veterinary Hospital, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia
| | - Zuzana Kostecká
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia
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Salivary metabolome of children and adolescents under peritoneal dialysis. Clin Oral Investig 2020; 25:2345-2351. [PMID: 32880015 DOI: 10.1007/s00784-020-03557-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/27/2020] [Indexed: 01/18/2023]
Abstract
OBJECTIVE To study the influence of peritoneal dialysis (PD) on the salivary metabolite profile of children and adolescents with renal failure. MATERIALS AND METHODS Healthy children/adolescents (n = 31; mean age: 12.18 ± 3.76) and children/adolescents subjected to PD (n = 12; mean age: 10.10 ± 4.25) were recruited. Oral health status assessed by the dmft/DMFT and Volpe-Manhold calculus indices. The 1H spectra were acquired in a 600-MHz Bruker nuclear magnetic resonance spectrometer and were subjected to multivariate analysis using partial least squares discriminant analysis (PLS-DA), orthogonal PLS-DA (O-PLS-DA), and univariate analysis through chi-square and t tests (SPSS 20.0, IL, USA), with a significance level of p < 0.05. RESULTS A similar caries pattern (p = 0.57; chi-square test) was observed between the healthy (dmft = 0.72 ± 1.28 and DMFT 0.93 ± 2.30) and PD groups (dmft = 2.14 ± 3.67, DMFT 0.33 ± 0.71) and dental calculus (p > 0.05, t test). PLS-DA and O-PLS-DA were able to distinguish both groups (ACC = 0.85, R2 = 0.80, Q2 = 0.15). Salivary metabolites decrease in creatine, propionate, and sugar levels in the PD group and an increase in creatinine, butyrate, and lactate levels when compared with the healthy group. CONCLUSIONS Children and adolescents subjected to PD have a different salivary metabolic profile from that of their healthy subjects. CLINICAL RELEVANCE Complications of peritoneal dialysis procedures could be monitored by proper knowledge of saliva characteristics as predictors of peritonitis-related outcome. The use of metabolomics in pediatric nephrology may be an innovative methodology for the early diagnosis and monitoring of kidney diseases.
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