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Cao X, Chen L, Lu K, Yu T, Xia H, Wang S, Sun G, Liu P, Liao W. Egg white-derived peptides reduced blood glucose in high-fat-diet and low-dose streptozotocin-induced type 2 diabetic mice via regulating the hepatic gluconeogenic signaling and metabolic profile. Food Funct 2024; 15:7003-7016. [PMID: 38855929 DOI: 10.1039/d4fo00725e] [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: 06/11/2024]
Abstract
Food proteins are considered an ideal source for the identification of bioactive peptides with the potential to intervene in nutrition-related chronic diseases such as cardiovascular disease, obesity, and diabetes. Egg white-derived peptides (EWPs) have been shown to improve glucose tolerance in insulin-resistant rats. However, underlying mechanisms are to be elucidated. Therefore, we hypothesized that EWP exerts a hypoglycemic effect by regulating hepatic glucose homeostasis. Our results showed that 7 weeks of EWP treatment reduced the fasting blood glucose in T2DM mice and the inhibition of the liver gluconeogenic pathway was involved in the mechanisms of actions. Using the untargeted metabolomics technique, we found that EWP treatment also altered the hepatic metabolic profile in T2DM mice, in which, the role of fatty acid esters of hydroxy fatty acids in mediating the hypoglycemic effect of EWPs might be pivotal.
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Affiliation(s)
- Xinyi Cao
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
| | - Liang Chen
- Public Service Platform of South China Sea for R&D Marine Biomedicine Resources, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Kun Lu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
| | - Tingqing Yu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
| | - Hui Xia
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
| | - Shaokang Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
| | - Guiju Sun
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
| | - Ping Liu
- Department of Food Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300, P.R. China
| | - Wang Liao
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P.R. China.
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Khan Q, Wang Y, Xia G, Yang H, Luo Z, Zhang Y. Deleterious Effects of Heat Stress on the Tomato, Its Innate Responses, and Potential Preventive Strategies in the Realm of Emerging Technologies. Metabolites 2024; 14:283. [PMID: 38786760 PMCID: PMC11122942 DOI: 10.3390/metabo14050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The tomato is a fruit vegetable rich in nutritional and medicinal value grown in greenhouses and fields worldwide. It is severely sensitive to heat stress, which frequently occurs with rising global warming. Predictions indicate a 0.2 °C increase in average surface temperatures per decade for the next three decades, which underlines the threat of austere heat stress in the future. Previous studies have reported that heat stress adversely affects tomato growth, limits nutrient availability, hammers photosynthesis, disrupts reproduction, denatures proteins, upsets signaling pathways, and damages cell membranes. The overproduction of reactive oxygen species in response to heat stress is toxic to tomato plants. The negative consequences of heat stress on the tomato have been the focus of much investigation, resulting in the emergence of several therapeutic interventions. However, a considerable distance remains to be covered to develop tomato varieties that are tolerant to current heat stress and durable in the perspective of increasing global warming. This current review provides a critical analysis of the heat stress consequences on the tomato in the context of global warming, its innate response to heat stress, and the elucidation of domains characterized by a scarcity of knowledge, along with potential avenues for enhancing sustainable tolerance against heat stress through the involvement of diverse advanced technologies. The particular mechanism underlying thermotolerance remains indeterminate and requires further elucidatory investigation. The precise roles and interplay of signaling pathways in response to heat stress remain unresolved. The etiology of tomato plants' physiological and molecular responses against heat stress remains unexplained. Utilizing modern functional genomics techniques, including transcriptomics, proteomics, and metabolomics, can assist in identifying potential candidate proteins, metabolites, genes, gene networks, and signaling pathways contributing to tomato stress tolerance. Improving tomato tolerance against heat stress urges a comprehensive and combined strategy including modern techniques, the latest apparatuses, speedy breeding, physiology, and molecular markers to regulate their physiological, molecular, and biochemical reactions.
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Affiliation(s)
| | | | | | | | | | - Yan Zhang
- Department of Landscape and Horticulture‚ Ecology College‚ Lishui University‚ Lishui 323000‚ China; (Q.K.); (Y.W.); (G.X.); (H.Y.); (Z.L.)
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3
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Zhang Y, Gan L, Tang J, Liu D, Chen G, Xu B. Metabolic profiling reveals new serum signatures to discriminate lupus nephritis from systemic lupus erythematosus. Front Immunol 2022; 13:967371. [PMID: 36059469 PMCID: PMC9437530 DOI: 10.3389/fimmu.2022.967371] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundLupus nephritis (LN) occurs in 50% of patients with systemic lupus erythematosus (SLE), causing considerable morbidity and even mortality. Previous studies had shown the potential of metabolic profiling in the diagnosis of SLE or LN. However, few metabonomics studies have attempted to distinguish SLE from LN based on metabolic changes. The current study was designed to find new candidate serum signatures that could differentiate LN from SLE patients using a non-targeted metabonomics method based on ultra high performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS).MethodMetabolic profiling of sera obtained from 21 healthy controls, 52 SLE patients and 43 LN patients. We used SPSS 25.0 for statistical analysis. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and metabolic pathway analysis were used to analyze the metabolic data.ResultsUpon comparison of SLE and LN groups, 28 differential metabolites were detected, the majority of which were lipids and amino acids. Glycerolphospholipid metabolism, pentose and glucuronate interconversions and porphyrin and chlorophyll metabolism were obviously enriched in LN patients versus those with SLE. Among the 28 characteristic metabolites, five key serum metabolites including SM d34:2, DG (18:3(9Z,12Z,15Z)/20:5(5Z,8Z,11Z,14Z,17Z)/0:0), nervonic acid, Cer-NS d27:4, and PC (18:3(6Z,9Z,12Z)/18:3(6Z,9Z,12Z) performed higher diagnostic performance in discriminating LN from SLE (all AUC > 0.75). Moreover, combined analysis of neuritic acid, C1q, and CysC (AUC = 0.916) produced the best combined diagnosis.ConclusionThis study identified five serum metabolites that are potential indicators for the differential diagnosis of SLE and LN. Glycerolphospholipid metabolism may play an important role in the development of SLE to LN. The metabolites we screened can provide more references for the diagnosis of LN and more support for the pathophysiological study of SLE progressed to LN.
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Affiliation(s)
- Yamei Zhang
- Department of Clinical Laboratory, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Lingling Gan
- Department of Clinical Laboratory, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Jie Tang
- Department of Clinical Laboratory, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Dan Liu
- Department of Pathology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Gang Chen
- Department of Clinical Laboratory, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Bei Xu
- Department of Clinical Laboratory, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
- *Correspondence: Gang Chen, ; Bei Xu,
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Liu B, Guo H, Li L, Geng Q, Zhao N, Tan Y, Nie Z, Ouyang G, Lu A, Lu C. Serum metabolomics analysis of deficiency pattern and excess pattern in patients with rheumatoid arthritis. Chin Med 2022; 17:71. [PMID: 35706052 PMCID: PMC9199155 DOI: 10.1186/s13020-022-00632-5] [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: 04/08/2022] [Accepted: 06/02/2022] [Indexed: 11/23/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a chronic and refractory autoimmune disease. Deficiency pattern (DP) and excess pattern (EP), as crucial types of Chinese medicine pattern diagnoses published by International Classification of Diseases 11th Revision (ICD-11), could provide new strategies for RA diagnosis. However, the biological basis of DP and EP of RA is not explicit. Methods 19 female RA DP patients, 41 female RA EP patients and 30 female healthy participants were included in the study. The serums of participants were collected and analyzed by metabolomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to profile metabolic characteristics of RA DP and EP. Furthermore, bioinformatics analysis results were obtained by using Ingenuity Pathway Analysis (IPA) and statistical analysis was performed by SAS version 9.4 for further identification of potential biomarkers. Results Serum metabolic profiling revealed 25 and 24 differential metabolites in RA DP and EP respectively, and 19 metabolites were common to RA DP and EP. Compared with DP group, L-Homocysteic acid, LysoPE(P-16:0/0:0), N(omega)-Hydroxyarginine and LysoPC(16:0/0:0) decreased (P < 0.05), and Pyruvic acid, D-Ribose, Gamma-Glutamylserine, PE(22:0/24:1(15Z)), Inosinic acid increased (P < 0.05) in EP group. Menawhile, S-Nitrosoglutathione, 5-Thymidylic acid, SN38 glucuronide, PE(22:0/24:0), PC(24:0/24:1(15Z)) and Bisdiphosphoinositol tetrakisphosphate increased significantly in DP group compared to EP group (P < 0.05). For the unique metabolites, bioinformatics analysis results showed that 5-Methoxytryptamine involved in Melatonin Degradation II and Superpathway of Melatonin Degradation is the key metabolite to RA DP. Meanwhile, GABA is the key metabolite in EP group, which involved in Glutamate Dependent Acid Resistance, GABA Receptor Signaling, Glutamate Degradation III (via 4-aminobutyrate) and 4-aminobutyrate Degradation I. Bioinformatics analysis between unique metabolites of RA DP and EP groups with human target genes for RA showed that 5-methoxytryptamine and LysoPC(18:1(9Z)/0:0), the unique metabolites of RA DP, might participate in colorectal cancer metastasis signaling, tumor microenvironment pathway, apoptosis signaling, MYC mediated apoptosis signaling, erythropoietin signaling pathway and LXR/RXR activation. Simultaneously, GABA, LysoPA(18:1(9Z)/0:0) and L-Targinine, the unique metabolites of RA EP, might participate in neuroinflammation signaling pathway, osteoarthritis pathway, glucocorticoid receptor signaling, ILK signaling, IL-17 signaling and HIF1α signaling. Conclusions The study indicates that serum metabolomics preliminarily revealed the biological basis of RA DP and EP. 5-methoxytryptamine, LysoPC(18:1(9Z)/0:0) and GABA, LysoPA(18:1(9Z)/0:0), L-Targinine might be the predictors to distinguish the DP and EP of RA respectively. These interesting results provide thoughts for further study of traditional medicine patterns of ICD-11. It also contributes to provide strategy for personalized precision treatment of RA and further validation is needed.
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Affiliation(s)
- Bin Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, 100700, China
| | - Hongtao Guo
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, 100700, China
| | - Qi Geng
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, 100700, China
| | - Ning Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, 100700, China
| | - Yong Tan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, 100700, China
| | - Zhixing Nie
- Shanghai Guanghua Hospital of Integreted Tranditional Chinese and Western Medicine, Shanghai, China
| | - Guilin Ouyang
- Shanghai Guanghua Hospital of Integreted Tranditional Chinese and Western Medicine, Shanghai, China
| | - Aiping Lu
- Shanghai Guanghua Hospital of Integreted Tranditional Chinese and Western Medicine, Shanghai, China. .,School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing, 100700, China.
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5
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Chen Y, Li EM, Xu LY. Guide to Metabolomics Analysis: A Bioinformatics Workflow. Metabolites 2022; 12:357. [PMID: 35448542 PMCID: PMC9032224 DOI: 10.3390/metabo12040357] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Metabolomics is an emerging field that quantifies numerous metabolites systematically. The key purpose of metabolomics is to identify the metabolites corresponding to each biological phenotype, and then provide an analysis of the mechanisms involved. Although metabolomics is important to understand the involved biological phenomena, the approach's ability to obtain an exhaustive description of the processes is limited. Thus, an analysis-integrated metabolomics, transcriptomics, proteomics, and other omics approach is recommended. Such integration of different omics data requires specialized statistical and bioinformatics software. This review focuses on the steps involved in metabolomics research and summarizes several main tools for metabolomics analyses. We also outline the most abnormal metabolic pathways in several cancers and diseases, and discuss the importance of multi-omics integration algorithms. Overall, our goal is to summarize the current metabolomics analysis workflow and its main analysis software to provide useful insights for researchers to establish a preferable pipeline of metabolomics or multi-omics analysis.
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Affiliation(s)
- Yang Chen
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041,
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6
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Wisgrill L, Fyhrquist N, Ndika J, Paalanen L, Berger A, Laatikainen T, Karisola P, Haahtela T, Alenius H. Bet v 1 triggers antiviral-type immune signaling in birch pollen allergic individuals. Clin Exp Allergy 2022; 52:929-941. [PMID: 35147263 PMCID: PMC9540660 DOI: 10.1111/cea.14108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/22/2022] [Accepted: 02/06/2022] [Indexed: 11/28/2022]
Abstract
Background In allergic patients, clinical symptoms caused by pollen remind of symptoms triggered by viral respiratory infections, which are also the main cause of asthmatic exacerbations. In patients sensitized to birch pollen, Bet v 1 is the major symptom‐causing allergen. Immune mechanisms driving Bet v 1‐related responses of human blood cells have not been fully characterized. Objective To characterize the immune response to Bet v 1 in peripheral blood in patients allergic to birch pollen. Methods The peripheral blood mononuclear cells of birch‐allergic (n = 24) and non‐allergic (n = 47) adolescents were stimulated ex‐vivo followed by transcriptomic profiling. Systems‐biology approaches were employed to decipher disease‐relevant gene networks and deconvolution of associated cell populations. Results Solely in birch‐allergic patients, co‐expression analysis revealed activation of networks of innate immunity and antiviral signalling as the immediate response to Bet v 1 stimulation. Toll‐like receptors and signal transducer transcription were the main drivers of gene expression patterns. Macrophages and dendritic cells were the main cell subsets responding to Bet v 1. Conclusions and clinical relevance In birch‐pollen‐allergic patients, the activated innate immune networks seem to be, in part, the same as those activated during viral infections. This tendency of the immune system to read pollens as viruses may provide new insight to allergy prevention and treatment.
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Affiliation(s)
- Lukas Wisgrill
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Human microbiome research program (HUMI), Medicum, University of Helsinki, Helsinki, Finland
| | - Joseph Ndika
- Human microbiome research program (HUMI), Medicum, University of Helsinki, Helsinki, Finland
| | - Laura Paalanen
- National Institute for Health and Welfare, Helsinki, Finland; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Angelika Berger
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Tiina Laatikainen
- National Institute for Health and Welfare, Helsinki, Finland; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Piia Karisola
- Human microbiome research program (HUMI), Medicum, University of Helsinki, Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Human microbiome research program (HUMI), Medicum, University of Helsinki, Helsinki, Finland
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7
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Dubey D, Kumar S, Rawat A, Guleria A, Kumari R, Ahmed S, Singh R, Misra R, Kumar D. NMR-Based Metabolomics Revealed the Underlying Inflammatory Pathology in Reactive Arthritis Synovial Joints. J Proteome Res 2021; 20:5088-5102. [PMID: 34661415 DOI: 10.1021/acs.jproteome.1c00620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reactive arthritis (ReA) is an aseptic synovitis condition that often develops 2-4 weeks after a distant (extra-articular) infection with Chlamydia, Salmonella, Shigella, Campylobacter, and Yersinia species. The metabolic changes in the synovial fluid (SF) may serve as indicative markers to both improve the diagnostic accuracy and understand the underlying inflammatory pathology of ReA. With this aim, the metabolic profiles of SF collected from ReA (n = 58) and non-ReA, i.e., rheumatoid arthritis (RA, n = 21) and osteoarthritis (OA, n = 20) patients, respectively, were measured using NMR spectroscopy and compared using orthogonal partial least-squares discriminant analysis (OPLS-DA). The discriminatory metabolic features were further evaluated for their diagnostic potential using the receiver operating characteristic (ROC) curve analysis. Compared to RA, two (alanine and carnitine), and compared to OA, six (NAG, glutamate, glycerol, isoleucine, alanine, and glucose) metabolic features were identified as diagnostic biomarkers. We further demonstrated the impact of ReA synovitis condition on the serum metabolic profiles through performing a correlation analysis. The Pearson rank coefficient (r) was estimated for 38 metabolites (profiled in both SF and serum samples obtained in pair from ReA patients) and was found significantly positive for 71% of the metabolites (r ranging from 0.17 to 0.87).
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Affiliation(s)
- Durgesh Dubey
- Centre of Biomedical Research, Lucknow 226014, India.,Department of Clinical Immunology & Rheumatology, SGPGIMS, Lucknow 226014, India
| | - Sandeep Kumar
- Department of Clinical Immunology & Rheumatology, SGPGIMS, Lucknow 226014, India
| | - Atul Rawat
- Centre of Biomedical Research, Lucknow 226014, India
| | | | - Reena Kumari
- Department of Biochemistry, KGMU, Lucknow 226003, India
| | - Sakir Ahmed
- Department of Clinical Immunology & Rheumatology, SGPGIMS, Lucknow 226014, India.,Department of Clinical Immunology and Rheumatology, KIMS, Bhubaneswar 751024, India
| | - Rajeev Singh
- Regional Medical Research Center, Gorakhpur 273013, India
| | - Ramnath Misra
- Department of Clinical Immunology & Rheumatology, SGPGIMS, Lucknow 226014, India.,Department of Clinical Immunology and Rheumatology, KIMS, Bhubaneswar 751024, India
| | - Dinesh Kumar
- Centre of Biomedical Research, Lucknow 226014, India
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8
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Zahoor I, Rui B, Khan J, Datta I, Giri S. An emerging potential of metabolomics in multiple sclerosis: a comprehensive overview. Cell Mol Life Sci 2021; 78:3181-3203. [PMID: 33449145 PMCID: PMC8038957 DOI: 10.1007/s00018-020-03733-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/14/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease of the nervous system that primarily affects young adults. Although the exact etiology of the disease remains obscure, it is clear that alterations in the metabolome contribute to this process. As such, defining a reliable and disease-specific metabolome has tremendous potential as a diagnostic and therapeutic strategy for MS. Here, we provide an overview of studies aimed at identifying the role of metabolomics in MS. These offer new insights into disease pathophysiology and the contributions of metabolic pathways to this process, identify unique markers indicative of treatment responses, and demonstrate the therapeutic effects of drug-like metabolites in cellular and animal models of MS. By and large, the commonly perturbed pathways in MS and its preclinical model include lipid metabolism involving alpha-linoleic acid pathway, nucleotide metabolism, amino acid metabolism, tricarboxylic acid cycle, d-ornithine and d-arginine pathways with collective role in signaling and energy supply. The metabolomics studies suggest that metabolic profiling of MS patient samples may uncover biomarkers that will advance our understanding of disease pathogenesis and progression, reduce delays and mistakes in diagnosis, monitor the course of disease, and detect better drug targets, all of which will improve early therapeutic interventions and improve evaluation of response to these treatments.
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Affiliation(s)
- Insha Zahoor
- Department of Neurology, Henry Ford Hospital, Detroit, MI, 48202, USA. .,Department of Neurology, Henry Ford Hospital, Education & Research Building, Room 4023, 2799 W Grand Blvd, Detroit, MI, 48202, USA.
| | - Bin Rui
- Department of Neurology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - Junaid Khan
- Department of Neurology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - Indrani Datta
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Shailendra Giri
- Department of Neurology, Henry Ford Hospital, Detroit, MI, 48202, USA. .,Department of Neurology, Henry Ford Hospital, Education & Research Building, Room 4051, 2799 W Grand Blvd, Detroit, MI, 48202, USA.
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9
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Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges. Eur Respir J 2020; 55:13993003.00844-2019. [PMID: 31619470 DOI: 10.1183/13993003.00844-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
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Affiliation(s)
- Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia .,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Peter D Sly
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Patrick G Holt
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Kathryn E Holt
- Dept of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Alan Turing Institute, London, UK
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10
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Lee SM, Lee EM, Park JK, Jeon HS, Oh S, Hong S, Jung YM, Kim BJ, Kim SM, Norwitz ER, Lee EB, Louangsenlath S, Park CW, Jun JK, Park JS, Lee DY. Metabolic Biomarkers In Midtrimester Maternal Plasma Can Accurately Predict Adverse Pregnancy Outcome in Patients with SLE. Sci Rep 2019; 9:15169. [PMID: 31645572 PMCID: PMC6811572 DOI: 10.1038/s41598-019-51285-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Patients with systemic lupus erythematosus (SLE) are at increased risk for adverse pregnancy outcome (APO). Accurate prediction of APO is critical to identify, counsel, and manage these high-risk patients. We undertook this study to identify novel biomarkers in mid-trimester maternal plasma to identify pregnant patients with SLE at increased risk of APOs. The study population consisted of pregnant women whose plasma was taken in mid-trimester and available for metabolic signature: (1) SLE and normal pregnancy outcome (Group 1, n = 21); (2) SLE with APO (Group 2, n = 12); and (3) healthy pregnant controls (Group 3, n = 10). Mid-trimester maternal plasma was analyzed for integrative profiles of primary metabolite and phospholipid using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) and liquid chromatography Orbitrap mass spectrometry (LC-Orbitrap MS). For performance comparison and validation, plasma samples were analyzed for sFlt-1/PlGF ratio. In the study population, APO developed in 12 of 33 women with SLE (36%). Metabolite profiling of mid-trimester maternal plasma samples identified a total of 327 metabolites using GC-TOF MS and LC-Orbitrap MS. Partial least squares discriminant analysis (PLS-DA) showed clear discrimination among the profiles of SLE groups and healthy pregnant controls (Groups 1/2 vs. 3). Moreover, direct comparison between Groups 1 and 2 demonstrated that 4 primary metabolites and 13 lipid molecules were significantly different. Binary logistic regression analysis suggested a potential metabolic biomarker model that could discriminate Groups 1 and 2. Receiver operating characteristic (ROC) analysis revealed the best predictability for APO with the combination model of two metabolites (LysoPC C22:5 and tryptophan) with AUC of 0.944, comparable to the AUC of sFlt-1/PlGF (AUC 0.857). In conclusion, metabolic biomarkers in mid-trimester maternal plasma can accurately predict APO in patients with SLE.
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Affiliation(s)
- Seung Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Mi Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, Korea
| | - Jin Kyun Park
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hae Sun Jeon
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Sohee Oh
- Department of Biostatistics, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Subeen Hong
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Young Mi Jung
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Byoung Jae Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea.,Department of Obstetrics and Gynecology, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sun Min Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea.,Department of Obstetrics and Gynecology, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Errol R Norwitz
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - Eun Bong Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | | | - Chan-Wook Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Joong Shin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea.
| | - Do Yup Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, Korea.
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11
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Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S. Food allergy and omics. J Allergy Clin Immunol 2019; 141:20-29. [PMID: 29307411 DOI: 10.1016/j.jaci.2017.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023]
Abstract
Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.
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Affiliation(s)
- Gopal Krishna Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Efren Rael
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Swati Acharya
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Stephen J Galli
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif
| | - Robert Tibshirani
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, Calif
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Holden Maecker
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Kari Christine Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif.
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
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12
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Løset M, Brown SJ, Saunes M, Hveem K. Genetics of Atopic Dermatitis: From DNA Sequence to Clinical Relevance. Dermatology 2019; 235:355-364. [PMID: 31203284 DOI: 10.1159/000500402] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/15/2019] [Indexed: 12/14/2022] Open
Abstract
Atopic dermatitis (AD) is a complex disease that is thought to be triggered by environmental factors in genetically susceptible individuals. Twin studies have estimated the heritability of AD to be approximately 75%, with the null (loss-of-function) mutations of the gene encoding filaggrin (FLG) (chromosome 1q21.3) as the strongest known genetic risk factor. The discovery of the filaggrin gene was important in the emerging model for AD pathogenesis, combining skin barrier function with adaptive and innate immunity. Assisted by the recent development of large-scale high-throughput genomics, more than 30 genetic loci have been linked to AD across different populations. Identification of these loci, together with functional studies, has already provided new insights into disease biology and identified novel drug targets. Further, these susceptibility loci are laying the groundwork for phenome-wide association studies to test their multiple phenotype relationships and application of Mendelian randomization to investigate causal relationships. Despite many known genes, a majority of the genetic risk for AD is yet unexplored. Therefore, studies investigating refined phenotype groups, low-frequency and rare genetic variation, gene-gene and/or gene-environment interactions, epigenetic mechanisms and data from multi-omics technologies are warranted. In this review, we describe genetic discoveries for AD, including results from candidate gene studies, studies of AD-like genetic diseases, genome-wide association studies and genetic sequencing studies. We explain how some of these genetic discoveries have unraveled new mechanistic insights into the pathogenesis of AD and exemplify how personal genetic data could be used for preventive strategies and a tailored treatment regimen (i.e., precision medicine).
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Affiliation(s)
- Mari Løset
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway, .,Department of Dermatology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway,
| | - Sara J Brown
- Skin Research Group, School of Medicine, University of Dundee, Dundee, United Kingdom.,Department of Dermatology, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Marit Saunes
- Department of Dermatology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Cancer Research and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
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13
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Kartsova LA, Solov’eva SA. Application of Chromatographic and Electrophoretic Techniques to Metabolomic Studies. JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1134/s1061934819040051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Dubey D, Chaurasia S, Guleria A, Kumar S, Modi DR, Misra R, Kumar D. Metabolite assignment of ultrafiltered synovial fluid extracted from knee joints of reactive arthritis patients using high resolution NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:30-43. [PMID: 29907975 DOI: 10.1002/mrc.4763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/27/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Currently, there are no reliable biomarkers available that can aid early differential diagnosis of reactive arthritis (ReA) from other inflammatory joint diseases. Metabolic profiling of synovial fluid (SF)-obtained from joints affected in ReA-holds great promise in this regard and will further aid monitoring treatment and improving our understanding about disease mechanism. As a first step in this direction, we report here the metabolite specific assignment of 1 H and 13 C resonances detected in the NMR spectra of SF samples extracted from human patients with established ReA. The metabolite characterization has been carried out on both normal and ultrafiltered (deproteinized) SF samples of eight ReA patients (n = 8) using high-resolution (800 MHz) 1 H and 1 H─13 C NMR spectroscopy methods such as one-dimensional 1 H CPMG and two-dimensional J-resolved1 H NMR and homonuclear 1 H─1 H TOCSY and heteronuclear1 H─13 C HSQC correlation spectra. Compared with normal SF samples, several distinctive 1 H NMR signals were identified and assigned to metabolites in the 1 H NMR spectra of ultrafiltered SF samples. Overall, we assigned 53 metabolites in normal filtered SF and 64 metabolites in filtered pooled SF sample compared with nonfiltered SF samples for which only 48 metabolites (including lipid/membrane metabolites as well) have been identified. The established NMR characterization of SF metabolites will serve to guide future metabolomics studies aiming to identify/evaluate the SF-based metabolic biomarkers of diagnostic/prognostic potential or seeking biochemical insights into disease mechanisms in a clinical perspective.
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Affiliation(s)
- Durgesh Dubey
- Centre of Biomedical Research, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
- Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Smriti Chaurasia
- Department of Clinical Immunology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Anupam Guleria
- Centre of Biomedical Research, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sandeep Kumar
- Department of Clinical Immunology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | | | - Ramnath Misra
- Department of Clinical Immunology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Dinesh Kumar
- Centre of Biomedical Research, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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15
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Guleria A, Phatak S, Dubey D, Kumar S, Zanwar A, Chaurasia S, Kumar U, Gupta R, Aggarwal A, Kumar D, Misra R. NMR-Based Serum Metabolomics Reveals Reprogramming of Lipid Dysregulation Following Cyclophosphamide-Based Induction Therapy in Lupus Nephritis. J Proteome Res 2018; 17:2440-2448. [PMID: 29877087 DOI: 10.1021/acs.jproteome.8b00192] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lupus nephritis (LN) is a major cause of morbidity and mortality in lupus. Renal biopsy is the gold standard for classification of nephritis, but because of its impracticality, new approaches for improving patient prognostication and monitoring treatment efficacy are needed. We aimed to evaluate the potential of metabolic profiling in identifying biomarkers to distinguish disease and monitor treatment efficacy in patients with LN. Serum samples from patients with LN ( n = 18) were profiled on NMR-based metabolomics platforms at diagnosis and after 6 months of treatment. LN patients had a different metabolomic fingerprint as compared with healthy controls, with increased lipoproteins and lipids and reduced acetate and amino acids. Using multivariate statistical analysis, we found that the metabolic changes observed in naïve LN patients at diagnosis displayed a variation in the opposite direction upon responding to treatment. Increased levels of lipid metabolites including low- and very-low-density lipoproteins (LDL/VLDL) in LN patients significantly decreased after 6 months of treatment, whereas the serum levels of acetate increased. These levels correlated significantly with SLE Disease Activity Index (SLEDAI 2K), renal SLEDAI, and serum C3 and C4 levels. The result presented in this pilot longitudinal study revealed the reprogramming of metabolome in LN patients on immunosuppressive therapy using NMR-based metabolomics, and thus this approach may be used to monitor the response to treatment.
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Affiliation(s)
- Anupam Guleria
- Centre of Biomedical Research , SGPGIMS Campus , Lucknow 226014 , India
| | - Sanat Phatak
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
| | - Durgesh Dubey
- Centre of Biomedical Research , SGPGIMS Campus , Lucknow 226014 , India
| | - Sandeep Kumar
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
| | - Abhishek Zanwar
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
| | - Smriti Chaurasia
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
| | - Umesh Kumar
- Centre of Biomedical Research , SGPGIMS Campus , Lucknow 226014 , India
| | - Ranjan Gupta
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
| | - Amita Aggarwal
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
| | - Dinesh Kumar
- Centre of Biomedical Research , SGPGIMS Campus , Lucknow 226014 , India
| | - Ramnath Misra
- Department of Clinical Immunology , SGPGIMS , Lucknow 226014 , India
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16
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Turi KN, Romick-Rosendale L, Ryckman KK, Hartert TV. A review of metabolomics approaches and their application in identifying causal pathways of childhood asthma. J Allergy Clin Immunol 2018; 141:1191-1201. [PMID: 28479327 PMCID: PMC5671382 DOI: 10.1016/j.jaci.2017.04.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/08/2017] [Accepted: 04/13/2017] [Indexed: 12/20/2022]
Abstract
Because asthma is a disease that results from host-environment interactions, an approach that allows assessment of the effect of the environment on the host is needed to understand the disease. Metabolomics has appealing potential as an application to study pathways to childhood asthma development. The objective of this review is to provide an overview of metabolomics methods and their application to understanding host-environment pathways in asthma development. We reviewed recent literature on advances in metabolomics and their application to study pathways to childhood asthma development. We highlight the (1) potential of metabolomics in understanding the pathogenesis of disease and the discovery of biomarkers; (2) choice of metabolomics techniques, biospecimen handling, and data analysis; (3) application to studying the role of the environment on asthma development; (4) review of metabolomics applied to the outcome of asthma; (5) recommendations for application of metabolomics-based -omics data integration in understanding disease pathogenesis; and (6) limitations. In conclusion, metabolomics allows use of biospecimens to identify useful biomarkers and pathways involved in disease development and subsequently to inform a greater understanding of disease pathogenesis and endotypes and prediction of the clinical course of childhood asthma phenotypes.
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Affiliation(s)
- Kedir N Turi
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn
| | - Lindsey Romick-Rosendale
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kelli K Ryckman
- Departments of Epidemiology and Pediatrics, College of Public Health and Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Tina V Hartert
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn.
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17
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LC-MS-based serum metabolomics reveals a distinctive signature in patients with rheumatoid arthritis. Clin Rheumatol 2018; 37:1493-1502. [DOI: 10.1007/s10067-018-4021-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/14/2018] [Accepted: 02/01/2018] [Indexed: 12/14/2022]
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18
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Zhao Y, Zhang J, Chen Y, Li Z, Nie H, Peng W, Su S. Altered Serum Metabolite Profiling and Relevant Pathway Analysis in Rats Stimulated by Honeybee Venom: New Insight into Allergy to Honeybee Venom. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:871-880. [PMID: 29322776 DOI: 10.1021/acs.jafc.7b04160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To improve our understanding of the disturbed metabolic pathways and cellular responses triggered by honeybee venom stimulation, we compared the changes in serum metabolites in rats, either stimulated or not by honeybee venom, by performing 1H nuclear magnetic resonance (NMR) spectrometry-based metabonomics to identify potential biomarkers. In this study, 65 metabolites were structurally confirmed and quantified and the following results were obtained. First, by pattern recognition analysis, 14 metabolites were selected as potential biomarkers 3 h after venom stimulation. Second, metabolic pathway analysis showed that methane metabolism, glyoxylate and dicarboxylate metabolism, tricarboxylic acid cycle, glycine, serine, and threonine metabolism, arginine and proline metabolism were affected. Finally, the time-dependent metabolic modifications indicated that rats could recover without medical treatment 24 h after venom stimulation. In summary, this new insight into the changes in serum metabolites in rats after honeybee venom stimulation has enhanced our understanding of the response of an organism to honeybee venom.
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Affiliation(s)
- Yazhou Zhao
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 100093, People's Republic of China
| | - Jianmei Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 100093, People's Republic of China
| | - Yanping Chen
- Bee Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA) , Beltsville, Maryland 20705, United States
| | - Zhiguo Li
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
| | - Hongyi Nie
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
| | - Wenjun Peng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 100093, People's Republic of China
| | - Songkun Su
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
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19
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Villaseñor A, Rosace D, Obeso D, Pérez-Gordo M, Chivato T, Barbas C, Barber D, Escribese MM. Allergic asthma: an overview of metabolomic strategies leading to the identification of biomarkers in the field. Clin Exp Allergy 2017; 47:442-456. [PMID: 28160515 DOI: 10.1111/cea.12902] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Allergic asthma is a prominent disease especially during childhood. Indoor allergens, in general, and particularly house dust mites (HDM) are the most prevalent sensitizers associated with allergic asthma. Available data show that 65-130 million people are mite-sensitized world-wide and as many as 50% of these are asthmatic. In fact, sensitization to HDM in the first years of life can produce devastating effects on pulmonary function leading to asthmatic syndromes that can be fatal. To date, there has been considerable research into the pathological pathways and structural changes associated with allergic asthma. However, limitations related to the disease heterogeneity and a lack of knowledge into its pathophysiology have impeded the generation of valuable data needed to appropriately phenotype patients and, subsequently, treat this disease. Here, we report a systematic and integral analysis of the disease, from airway remodelling to the immune response taking place throughout the disease stages. We present an overview of metabolomics, the management of complex multifactorial diseases through the analysis of all possible metabolites in a biological sample, obtaining a global interpretation of biological systems. Special interest is placed on the challenges to obtain biological samples and the methodological aspects to acquire relevant information, focusing on the identification of novel biomarkers associated with specific phenotypes of allergic asthma. We also present an overview of the metabolites cited in the literature, which have been related to inflammation and immune response in asthma and other allergy-related diseases.
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Affiliation(s)
- A Villaseñor
- Faculty of Medicine, Institute of Applied Molecular Medicine (IMMA), CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - D Rosace
- Faculty of Medicine, Institute of Applied Molecular Medicine (IMMA), CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - D Obeso
- Faculty of Medicine, Institute of Applied Molecular Medicine (IMMA), CEU San Pablo University, Boadilla del Monte, Madrid, Spain.,Faculty of Pharmacy, Centre for Metabolomics and Bioanalysis (CEMBIO), CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - M Pérez-Gordo
- Faculty of Pharmacy, Centre for Metabolomics and Bioanalysis (CEMBIO), CEU San Pablo University, Boadilla del Monte, Madrid, Spain.,Basic Medical Sciences Department, Faculty of Medicine, CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - T Chivato
- Basic Medical Sciences Department, Faculty of Medicine, CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - C Barbas
- Faculty of Pharmacy, Centre for Metabolomics and Bioanalysis (CEMBIO), CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - D Barber
- Faculty of Medicine, Institute of Applied Molecular Medicine (IMMA), CEU San Pablo University, Boadilla del Monte, Madrid, Spain
| | - M M Escribese
- Faculty of Medicine, Institute of Applied Molecular Medicine (IMMA), CEU San Pablo University, Boadilla del Monte, Madrid, Spain.,Basic Medical Sciences Department, Faculty of Medicine, CEU San Pablo University, Boadilla del Monte, Madrid, Spain
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20
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Shin TH, Kim HA, Jung JY, Baek WY, Lee HS, Park HJ, Min J, Paik MJ, Lee G, Suh CH. Analysis of the free fatty acid metabolome in the plasma of patients with systemic lupus erythematosus and fever. Metabolomics 2017; 14:14. [PMID: 30830319 DOI: 10.1007/s11306-017-1308-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/08/2017] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease with heterogeneous clinical manifestations mediated by immune dysregulation. OBJECTIVES We aimed to analyze the metabolomic differences in free fatty acids (FFAs) between patients with SLE and healthy controls (HCs). METHODS In this study, the levels of 24 FFAs, as their tert-butyldimethylsilyl derivatives, in the plasma of 41 patients with SLE and 41 HCs, were investigated using gas chromatography with mass spectrometry in selected-ion monitoring mode. RESULTS The results showed that patients with SLE and HCs had significantly different levels of 13 of the 24 FFAs. The levels of myristic, palmitoleic, oleic, and eicosenoic acids were significantly higher, whereas the levels of caproic, caprylic, linoleic, stearic, arachidonic, eicosanoic, behenic, lignoceric, and hexacosanoic acids were significantly lower in patients with SLE, than in the HCs. In the partial-correlation analysis of the FFA profiles and markers of disease activity of SLE, several metabolic markers correlated with SLE disease activity. CONCLUSIONS Our results provide a comprehensive understanding of the relationship between FFAs and markers of SLE disease activity. Thus, this approach has promising potential for the discovery of metabolic biomarkers of SLE.
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Affiliation(s)
- Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Hyoun-Ah Kim
- Department of Rheumatology and BK21 Division of Cell Transformation and Restoration, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Ju-Yang Jung
- Department of Rheumatology and BK21 Division of Cell Transformation and Restoration, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Wook-Young Baek
- Department of Rheumatology and BK21 Division of Cell Transformation and Restoration, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Hyeon-Seong Lee
- Department of Physiology, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Hyung Jin Park
- Department of Physiology, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Jeuk Min
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Man-Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, 164, World cup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea.
| | - Chang-Hee Suh
- Department of Rheumatology and BK21 Division of Cell Transformation and Restoration, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, 16499, Republic of Korea.
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21
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Ahn JK, Kim J, Hwang J, Song J, Kim KH, Cha HS. Potential metabolomic biomarkers for reliable diagnosis of Behcet's disease using gas chromatography/ time-of-flight-mass spectrometry. Joint Bone Spine 2017; 85:337-343. [PMID: 28549946 DOI: 10.1016/j.jbspin.2017.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Although many diagnostic criteria of Behcet's disease (BD) have been developed and revised by experts, diagnosing BD is still complicated and challenging. No metabolomic studies on serum have been attempted to improve the diagnosis and to identify potential biomarkers of BD. The purposes of this study were to investigate distinctive metabolic changes in serum samples of BD patients and to identify metabolic candidate biomarkers for reliable diagnosis of BD using the metabolomics platform. METHODS Metabolomic profiling of 90 serum samples from 45 BD patients and 45 healthy controls (HCs) were performed via gas chromatography with time-of-flight mass spectrometry (GC/TOF-MS) with multivariate statistical analyses. RESULTS A total of 104 metabolites were identified from samples. The serum metabolite profiles obtained from GC/TOF-MS analysis can distinguish BD patients from HC group in discovery set. The variation values of the partial least squared-discrimination analysis (PLS-DA) model are R2X of 0.246, R2Y of 0.913 and Q2 of 0.852, respectively, indicating strong explanation and prediction capabilities of the model. A panel of five metabolic biomarkers, namely, decanoic acid, fructose, tagatose, linoleic acid and oleic acid were selected and adequately validated as putative biomarkers of BD (sensitivity 100%, specificity 97.1%, area under the curve 0.998) in the discovery set and independent set. The PLS_DA model showed clear discrimination of BD and HC groups by the five metabolic biomarkers in independent set. CONCLUSIONS This is the first report on characteristic metabolic profiles and potential metabolite biomarkers in serum for reliable diagnosis of BD using GC/TOF-MS.
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Affiliation(s)
- Joong Kyong Ahn
- Division of Rheumatology, Department of Internal medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, 03181 Seoul, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, 02841 Seoul, Republic of Korea
| | - Jiwon Hwang
- Department of Internal medicine, National Police Hospital, 05715 Seoul, Republic of Korea
| | - Juhwan Song
- Department of Biotechnology, Graduate School, Korea University, 02841 Seoul, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, 02841 Seoul, Republic of Korea.
| | - Hoon-Suk Cha
- Division of Rheumatology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 06351 Seoul, Republic of Korea.
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Li J, Xie XW, Zhou H, Wang B, Zhang MJ, Tang FY. Metabolic profiling reveals new serum biomarkers of lupus nephritis. Lupus 2017; 26:1166-1173. [PMID: 28420061 DOI: 10.1177/0961203317694256] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics has been applied to explore altered metabolite profiles in disease and identify unique metabolic signatures specific to certain pathologies. The aim of the current study is to characterize the metabolic profile of patients diagnosed with lupus nephritis (LN) and explore new insights into underlying disease processes. A metabolomic approach using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) was developed in serum samples from 32 LN patients, 30 idiopathic nephrotic syndrome (INS) patients and 28 healthy controls (HCs). Potential biomarkers were screened from orthogonal projection to latent structures discriminate analysis (OPLS-DA) and further evaluated by receiver operating characteristic analysis (ROC). A total of 14 potential biomarkers were screened and tentatively identified for LN patients compared to HCs. Compared to HCs and INS patients, the LN patients had increased serum levels of sorbitol and glycocholic acid metabolites and decreased levels of cortisol, creatinine and L-aspartyl-L-phenylalanine. A panel of three metabolomics (theophylline, oxidized glutathione and capric acid) was identified as biomarkers of LN with a sensitivity of 87.50% and a specificity of 67.86% using ROC analysis. Our results suggest that UPLC-HRMS based quantification of circulating metabolites was a useful tool for identification of biomarkers with the ability to segregate LN patients from INS patients and HCs. The potential biomarkers indicated that the LN metabolic disturbance may be closely associated with inflammation injury, oxidative stress and phospholipid metabolism.
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Affiliation(s)
- J Li
- Department of Rheumatology, Huai’an First People’s Hospital, Nanjing Medical University, Huai’an, Jiangsu, P.R. China
- Department of Rheumatology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - X-W Xie
- Department of Cardiology, Huai’an First People’s Hospital, Nanjing Medical University, Huai’an, Jiangsu, P.R. China
| | - H Zhou
- Department of Nephrology, Huai’an First People’s Hospital, Nanjing Medical University, Huai’an, Jiangsu, P.R. China
| | - B Wang
- Department of Clinical Laboratory, Huai’an First People’s Hospital, Nanjing Medical University, Huai’an, Jiangsu, China
| | - M-J Zhang
- Department of Rheumatology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - F-Y Tang
- Department of Nephrology, Huai’an First People’s Hospital, Nanjing Medical University, Huai’an, Jiangsu, P.R. China
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Metabolic Disturbances in Adult-Onset Still's Disease Evaluated Using Liquid Chromatography/Mass Spectrometry-Based Metabolomic Analysis. PLoS One 2016; 11:e0168147. [PMID: 28005947 PMCID: PMC5179000 DOI: 10.1371/journal.pone.0168147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/25/2016] [Indexed: 11/25/2022] Open
Abstract
Objective Liquid chromatography/mass spectrometry (LC/MS)-based comprehensive analysis of metabolic profiles with metabolomics approach has potential diagnostic and predictive implications. However, no metabolomics data have been reported in adult-onset Still’s disease (AOSD). This study investigated the metabolomic profiles in AOSD patients and examined their association with clinical characteristics and disease outcome. Methods Serum metabolite profiles were determined on 32 AOSD patients and 30 healthy controls (HC) using ultra-performance liquid chromatography (UPLC)/MS analysis, and the differentially expressed metabolites were quantified using multiple reactions monitoring (MRM)/MS analysis in 44 patients and 42 HC. Pure standards were utilized to confirm the presence of the differentially expressed metabolites. Results Eighteen differentially expressed metabolites were identified in AOSD patents using LC/MS-based analysis, of which 13 metabolites were validated by MRM/MS analysis. Among them, serum levels of lysoPC(18:2), urocanic acid and indole were significantly lower, and L-phenylalanine levels were significantly higher in AOSD patients compared with HC. Moreover, serum levels of lysoPC(18:2), PhePhe, uridine, taurine, L-threonine, and (R)-3-Hydroxy-hexadecanoic acid were significantly correlated with disease activity scores (all p<0.05) in AOSD patients. A different clustering of metabolites was associated with a different disease outcome, with significantly lower levels of isovalerylsarcosine observed in patients with chronic articular pattern (median, 77.0AU/ml) compared with monocyclic (341.5AU/ml, p<0.01) or polycyclic systemic pattern (168.0AU/ml, p<0.05). Conclusion Thirteen differentially expressed metabolites identified and validated in AOSD patients were shown to be involved in five metabolic pathways. Significant associations of metabolic profiles with disease activity and outcome of AOSD suggest their involvement in AOSD pathogenesis.
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NMR based serum metabolomics reveals a distinctive signature in patients with Lupus Nephritis. Sci Rep 2016; 6:35309. [PMID: 27739464 PMCID: PMC5064370 DOI: 10.1038/srep35309] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/27/2016] [Indexed: 01/12/2023] Open
Abstract
Management of patient with Lupus Nephritis (LN) continues to remain a challenge for the treating physicians because of considerable morbidity and even mortality. The search of biomarkers in serum and urine is a focus of researchers to unravel new targets for therapy. In the present study, the utility of NMR-based serum metabolomics has been evaluated for the first time in discriminating LN patients from non-nephritis lupus patients (SLE) and further to get new insights into the underlying disease processes for better clinical management. Metabolic profiling of sera obtained from 22 SLE patients, 40 LN patients and 30 healthy controls (HC) were performed using high resolution 1D 1H-CPMG and diffusion edited NMR spectra to identify the potential molecular biomarkers. Using multivariate analysis, we could distinguish SLE and LN patients from HC and LN from SLE patients. Compared to SLE patients, the LN patients had increased serum levels of lipid metabolites (including LDL/VLDL lipoproteins), creatinine and decreased levels of acetate. Our results revealed that metabolic markers especially lipids and acetate derived from NMR spectroscopy has high sensitivity and specificity to distinguish LN among SLE patients and has the potential to be a useful adjunctive tool in diagnosis and clinical management of LN.
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Fei H, Hou J, Wu Z, Zhang L, Zhao H, Dong X, Chen Y. Plasma metabolomic profile and potential biomarkers for missed abortion. Biomed Chromatogr 2016; 30:1942-1952. [PMID: 27229294 DOI: 10.1002/bmc.3770] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/13/2016] [Accepted: 05/20/2016] [Indexed: 01/08/2023]
Abstract
A missed abortion (MA) is an in utero death of the embryo or fetus before the 20th week of gestation with retained products of conception, and this condition is currently common in China. In order to discover novel biomarkers for MA, ultrahigh performance liquid chromatography was applied to study plasma metabolite profiles for 33 patients with MA and 29 control subjects. Thirty-seven differential plasma metabolites were found to discriminate between the two groups in the initial cohort (15 subjects with MA and 15 healthy controls). The feasibility of using these potential biomarkers to predict MA was further evaluated in the validation cohort (18 subjects with MA and 14 healthy controls) and 15 had an area under the receiver operating characteristic curve of >0.80, making them satisfactory. Tryptophan metabolism and sphingolipid metabolism were identified as important potential target pathways for MA using metabolic pathway impact analysis. Furthermore, three of the 15 satisfactory metabolites (glyceric acid, indole and sphingosine) were combined to establish a predictive model with 100% sensitivity and 100% specificity in the validation cohort. Taken together, these results suggest that MA results in significant disturbance of metabolism and those various novel biomarkers have satisfactory diagnostic and predictive power for MA.
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Affiliation(s)
- He Fei
- Department of Obstetrics and Gynaecology, The Fifth People's Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, People's Republic of China
| | - Jiebin Hou
- Second Military Medical University, Shanghai, People's Republic of China
| | - Zhenghong Wu
- Department of Obstetrics and Gynaecology, The Fifth People's Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, People's Republic of China
| | - Liwen Zhang
- Department of Obstetrics and Gynaecology, The Fifth People's Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, People's Republic of China
| | - Hongxia Zhao
- Second Military Medical University, Shanghai, People's Republic of China
| | - Xin Dong
- Second Military Medical University, Shanghai, People's Republic of China
| | - Yaping Chen
- Department of Obstetrics and Gynaecology, The Fifth People's Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, People's Republic of China
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Frohnert BI, Rewers MJ. Metabolomics in childhood diabetes. Pediatr Diabetes 2016; 17:3-14. [PMID: 26420304 PMCID: PMC4703499 DOI: 10.1111/pedi.12323] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 12/30/2022] Open
Abstract
Recent increases in the incidence of both type 1 (T1D) and type 2 diabetes (T2D) in children and adolescents point to the importance of environmental factors in the development of these diseases. Metabolomic analysis explores the integrated response of the organism to environmental changes. Metabolic profiling can identify biomarkers that are predictive of disease incidence and development, potentially providing insight into disease pathogenesis. This review provides an overview of the role of metabolomic analysis in diabetes research and summarizes recent research relating to the development of T1D and T2D in children.
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Affiliation(s)
- Brigitte I Frohnert
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CO 80045 USA
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CO 80045 USA
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27
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Lu X, Lian X, zheng J, Ai N, Ji C, Hao C, Fan X. LC-ESI-TOF-MS-based metabolomic analysis of ginsenoside Rd-induced anaphylactoid reaction in mice. RSC Adv 2016. [DOI: 10.1039/c5ra24301g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A ginsenoside Rd-induced anaphylactoid reaction in mice was investigated by LC-ESI-TOF-MS-based metabolomic analysis as well as general toxicological assessments.
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Affiliation(s)
- Xiaoyan Lu
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Xueping Lian
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Jie zheng
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Ni Ai
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Cai Ji
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Cui Hao
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou 310058
- China
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Priori R, Casadei L, Valerio M, Scrivo R, Valesini G, Manetti C. ¹H-NMR-Based Metabolomic Study for Identifying Serum Profiles Associated with the Response to Etanercept in Patients with Rheumatoid Arthritis. PLoS One 2015; 10:e0138537. [PMID: 26558759 PMCID: PMC4641599 DOI: 10.1371/journal.pone.0138537] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/01/2015] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE A considerable proportion of patients with rheumatoid arthritis (RA) do not have a satisfactory response to biological therapies. We investigated the use of metabolomics approach to identify biomarkers able to anticipate the response to biologics in RA patients. METHODS Due to gender differences in metabolomic profiling, the analysis was restricted to female patients starting etanercept as the first biological treatment and having a minimum of six months' follow-up. Each patient was evaluated by the same rheumatologist before and after six months of treatment. At this time, the clinical response (good, moderate, none) was determined according to the EUropean League Against Rheumatism (EULAR) criteria, based on both erythrocyte sedimentation rate (EULAR-ESR) and C-reactive protein (EULAR-CRP). Sera collected prior and after six months of etanercept were analyzed by 1H-nuclear magnetic resonance (NMR) spectroscopy in combination with multivariate data analysis. RESULTS Twenty-seven patients were enrolled: 18 had a good/moderate response and 9 were non responders according to both EULAR-ESR and EULAR-CRP after six months of etanercept. Metabolomic analysis at baseline was able to discriminate good, moderate, and non-responders with a very good predictivity (Q2 = 0.68) and an excellent sensitivity, specificity, and accuracy (100%). In good responders, we found an increase in isoleucine, leucine, valine, alanine, glutamine, tyrosine, and glucose levels and a decrease in 3-hydroxybutyrate levels after six months of treatment with etanercept with respect to baseline. CONCLUSION Our study confirms the potential of metabolomic analysis to predict the response to biological agents. Changes in metabolic profiles during treatment may help elucidate their mechanism of action.
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Affiliation(s)
- Roberta Priori
- Department of Internal Medicine and Medical Specialties—Rheumatology Unit, Sapienza University of Rome, Rome, Italy
| | - Luca Casadei
- Department of Chemistry—Sapienza University of Rome, Rome, Italy
| | | | - Rossana Scrivo
- Department of Internal Medicine and Medical Specialties—Rheumatology Unit, Sapienza University of Rome, Rome, Italy
| | - Guido Valesini
- Department of Internal Medicine and Medical Specialties—Rheumatology Unit, Sapienza University of Rome, Rome, Italy
- * E-mail:
| | - Cesare Manetti
- Department of Chemistry—Sapienza University of Rome, Rome, Italy
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Colvin KL, Yeager ME. Proteomics of pulmonary hypertension: could personalized profiles lead to personalized medicine? Proteomics Clin Appl 2015; 9:111-20. [PMID: 25408474 DOI: 10.1002/prca.201400157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/13/2014] [Accepted: 11/13/2014] [Indexed: 12/12/2022]
Abstract
Pulmonary hypertension (PH) is a fatal syndrome that arises from a multifactorial and complex background, is characterized by increased pulmonary vascular resistance and right heart afterload, and often leads to cor pulmonale. Over the past decades, remarkable progress has been made in reducing patient symptoms and delaying the progression of the disease. Unfortunately, PH remains a disease with no cure. The substantial heterogeneity of PH continues to be a major limitation to the development of newer and more efficacious therapies. New advances in our understanding of the biological pathways leading to such a complex pathogenesis will require the identification of the important proteins and protein networks that differ between a healthy lung (or right ventricle) and a remodeled lung in an individual with PH. In this article, we present the case for the increased use of proteomics--the study of proteins and protein networks--as a discovery tool for key proteins and protein networks operational in the PH lung. We review recent applications of proteomics in PH, and summarize the biological pathways identified. Finally, we attempt to presage what the future will bring with regard to proteomics in PH and offer our perspectives on the prospects of developing personalized proteomics and custom-tailored therapies.
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Affiliation(s)
- Kelley L Colvin
- Department of Pediatrics-Critical Care, University of Colorado Denver, Aurora, CO, USA; Cardiovascular Pulmonary Research, University of Colorado Denver, Aurora, CO, USA; Department of Bioengineering, University of Colorado Denver, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Denver, Aurora, CO, USA
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Ahn JK, Kim S, Kim J, Hwang J, Kim KH, Cha HS. A Comparative Metabolomic Evaluation of Behcet's Disease with Arthritis and Seronegative Arthritis Using Synovial Fluid. PLoS One 2015; 10:e0135856. [PMID: 26270538 PMCID: PMC4536180 DOI: 10.1371/journal.pone.0135856] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 07/08/2015] [Indexed: 12/22/2022] Open
Abstract
Behcet’s disease (BD) with arthritis is often confused with seronegative arthritis (SNA) because of shared clinical symptoms and the lack of definitive biomarkers for BD. To investigate possible metabolic patterns and potential biomarkers of BD with arthritis, metabolomic profiling of synovial fluid (SF) from 6 patients with BD with arthritis and 18 patients with SNA was performed using gas chromatography/time-of-flight mass spectrometry in conjunction with univariate and multivariate statistical analyses. A total of 123 metabolites were identified from samples. Orthogonal partial least square-discriminant analysis showed clear discrimination between BD with arthritis and SNA. A set of 11 metabolites were identified as potential biomarkers for BD using variable importance for projection values and the Wilcoxon-Mann-Whitney test. Compared with SNA, BD with arthritis exhibited relatively high levels of glutamate, valine, citramalate, leucine, methionine sulfoxide, glycerate, phosphate, lysine, isoleucine, urea, and citrulline. There were two markers identified, elevated methionine sulfoxide and citrulline, that were associated with increased oxidative stress, providing a potential link to BD-associated neutrophil hyperactivity. Glutamate, citramalate, and valine were selected and validated as putative biomarkers for BD with arthritis (sensitivity, 100%; specificity, 61.1%). This is the first report to present potential biomarkers from SF for discriminating BD with arthritis from SNA. The metabolomics of SF may be helpful in searching for potential biomarkers and elucidating the clinicopathogenesis of BD with arthritis.
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Affiliation(s)
- Joong Kyong Ahn
- Department of Internal Medicine, Division of Rheumatology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sooah Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Jiwon Hwang
- Department of Internal Medicine, Division of Rheumatology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
- * E-mail: (HSC); (KHK)
| | - Hoon-Suk Cha
- Department of Medicine, Division of Rheumatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- * E-mail: (HSC); (KHK)
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Guleria A, Misra DP, Rawat A, Dubey D, Khetrapal CL, Bacon P, Misra R, Kumar D. NMR-Based Serum Metabolomics Discriminates Takayasu Arteritis from Healthy Individuals: A Proof-of-Principle Study. J Proteome Res 2015; 14:3372-81. [PMID: 26081138 DOI: 10.1021/acs.jproteome.5b00422] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Takayasu arteritis (TA) is a debilitating, systemic disease that involves the aorta and large arteries in a chronic inflammatory process that leads to vessel stenosis. Initially, the disease remains clinically silent (or remains undetected) until the patients present with vascular occlusion. Therefore, new methods for appropriate and timely diagnosis of TA cases are needed to start proper therapy on time and also to monitor the patient's response to the given treatment. In this context, NMR-based serum metabolomic profiling has been explored in this proof-of-principle study for the first time to determine characteristic metabolites that could be potentially helpful for diagnosis and prognosis of TA. Serum metabolic profiling of TA patients (n = 29) and healthy controls (n = 30) was performed using 1D (1)H NMR spectroscopy, and possible biomarker metabolites were identified. Using projection to least-squares discriminant analysis, we could distinguish TA patients from healthy controls. Compared to healthy controls, TA patients had (a) increased serum levels of choline metabolites, LDL cholesterol, N-acetyl glycoproteins (NAGs), and glucose and (b) decreased serum levels of lactate, lipids, HDL cholesterol, and glucogenic amino acids. The results of this study are preliminary and need to be confirmed in a prospective study.
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Affiliation(s)
- Anupam Guleria
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Durga Prasanna Misra
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Atul Rawat
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Durgesh Dubey
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Chunni Lal Khetrapal
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Paul Bacon
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ramnath Misra
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Dinesh Kumar
- †Centre of Biomedical Research and ‡Department of Immunology, SGPGIMS, Lucknow, 226014 Uttar Pradesh, India.,§Rheumatology Research Group, Division of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
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Kim HA, Jung JY, Suh CH. Biomarkers for systemic lupus erythematosus: an update. ACTA ACUST UNITED AC 2015. [DOI: 10.2217/ijr.15.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Yin XH, Huang GL, Lin DR, Wan CC, Wang YD, Song JK, Xu P. Exposure to fluoride in drinking water and hip fracture risk: a meta-analysis of observational studies. PLoS One 2015; 10:e0126488. [PMID: 26020536 PMCID: PMC4447426 DOI: 10.1371/journal.pone.0126488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 04/06/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Many observational studies have shown that exposure to fluoride in drinking water is associated with hip fracture risk. However, the findings are varied or even contradictory. In this work, we performed a meta-analysis to assess the relationship between fluoride exposure and hip fracture risk. METHODS PubMed and EMBASE databases were searched to identify relevant observational studies from the time of inception until March 2014 without restrictions. Data from the included studies were extracted and analyzed by two authors. Summary relative risks (RRs) with corresponding 95% confidence intervals (CIs) were pooled using random- or fixed-effects models as appropriate. Sensitivity analyses and meta-regression were conducted to explore possible explanations for heterogeneity. Finally, publication bias was assessed. RESULTS Fourteen observational studies involving thirteen cohort studies and one case-control study were included in the meta-analysis. Exposure to fluoride in drinking water does not significantly increase the incidence of hip fracture (RRs, 1.05; 95% CIs, 0.96-1.15). Sensitivity analyses based on adjustment for covariates, effect measure, country, sex, sample size, quality of Newcastle-Ottawa Scale scores, and follow-up period validated the strength of the results. Meta-regression showed that country, gender, quality of Newcastle-Ottawa Scale scores, adjustment for covariates and sample size were not sources of heterogeneity. Little evidence of publication bias was observed. CONCLUSION The present meta-analysis suggests that chronic fluoride exposure from drinking water does not significantly increase the risk of hip fracture. Given the potential confounding factors and exposure misclassification, further large-scale, high-quality studies are needed to evaluate the association between exposure to fluoride in drinking water and hip fracture risk.
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Affiliation(s)
- Xin-Hai Yin
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
| | - Guang-Lei Huang
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
| | - Du-Ren Lin
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
| | - Cheng-Cheng Wan
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
| | - Ya-Dong Wang
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
| | - Ju-Kun Song
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
- * E-mail:
| | - Ping Xu
- Department of Oral and Maxillary Surgery, Gui Zhou provincial people's hospital, Guiyang, Gui Zhou, PR China
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Systems biology of asthma and allergic diseases: a multiscale approach. J Allergy Clin Immunol 2014; 135:31-42. [PMID: 25468194 DOI: 10.1016/j.jaci.2014.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/10/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Abstract
Systems biology is an approach to understanding living systems that focuses on modeling diverse types of high-dimensional interactions to develop a more comprehensive understanding of complex phenotypes manifested by the system. High-throughput molecular, cellular, and physiologic profiling of populations is coupled with bioinformatic and computational techniques to identify new functional roles for genes, regulatory elements, and metabolites in the context of the molecular networks that define biological processes associated with system physiology. Given the complexity and heterogeneity of asthma and allergic diseases, a systems biology approach is attractive, as it has the potential to model the myriad connections and interdependencies between genetic predisposition, environmental perturbations, regulatory intermediaries, and molecular sequelae that ultimately lead to diverse disease phenotypes and treatment responses across individuals. The increasing availability of high-throughput technologies has enabled system-wide profiling of the genome, transcriptome, epigenome, microbiome, and metabolome, providing fodder for systems biology approaches to examine asthma and allergy at a more holistic level. In this article we review the technologies and approaches for system-wide profiling, as well as their more recent applications to asthma and allergy. We discuss approaches for integrating multiscale data through network analyses and provide perspective on how individually captured health profiles will contribute to more accurate systems biology views of asthma and allergy.
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35
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Genetics, environment, and gene-environment interactions in the development of systemic rheumatic diseases. Rheum Dis Clin North Am 2014; 40:637-57. [PMID: 25437282 DOI: 10.1016/j.rdc.2014.07.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rheumatic diseases offer distinct challenges to researchers because of heterogeneity in disease phenotypes, low disease incidence, and geographic variation in genetic and environmental factors. Emerging research areas, including epigenetics, metabolomics, and the microbiome, may provide additional links between genetic and environmental risk factors in the pathogenesis of rheumatic disease. This article reviews the methods used to establish genetic and environmental risk factors and studies gene-environment interactions in rheumatic diseases, and provides specific examples of successes and challenges in identifying gene-environment interactions in rheumatoid arthritis, systemic lupus erythematosus, and ankylosing spondylitis. Emerging research strategies and future challenges are discussed.
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Li P, Cui BT, Duan YN, Zhang FM. Laboratory evaluation and metabolomics in inflammatory bowel disease. Shijie Huaren Xiaohua Zazhi 2014; 22:3592-3599. [DOI: 10.11569/wcjd.v22.i24.3592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diagnosis and prognosis of inflammatory bowel disease (IBD) remain a challenge for physicians, and they are often based on history, clinical symptoms and endoscopic, histological, radiological and laboratory findings. Studies have shown that metabolomics may have important value in the diagnosis and prognosis of IBD. This paper will review the latest progress in laboratory evaluation and metabolomics in IBD.
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