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Xu Y, Ding K, Peng Z, Ding L, Li H, Fan Y. Evaluating for Correlations between Specific Metabolites in Patients Receiving First-Line or Second-Line Immunotherapy for Metastatic or Recurrent NSCLC: An Exploratory Study Based on Two Cohorts. Mol Cancer Ther 2024; 23:733-742. [PMID: 38346938 PMCID: PMC11063768 DOI: 10.1158/1535-7163.mct-23-0459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 11/07/2023] [Accepted: 02/06/2024] [Indexed: 05/03/2024]
Abstract
Immune checkpoint inhibitors (ICI) have displayed impressive clinical efficacy in the context of non-small cell lung cancer (NSCLC). However, most patients do not achieve long-term survival. Minimally invasive collected samples are attracting significant interest as new fields of biomarker study, and metabolomics is one of these growing fields. We concentrated on the augmented value of the metabolomic profile in differentiating long-term survival from short-term survival in patients with NSCLC subjected to ICIs. We prospectively recruited 97 patients with stage IV NSCLC who were treated with anti-PD-1 inhibitor, including patients treated with monoimmunotherapy as second-line treatment (Cohort 1), and patients treated with combination immunotherapy as first-line treatment (Cohort 2). Each cohort was divided into long-term and short-term survival groups. All blood samples were collected before beginning immunotherapy. Serum metabolomic profiling was performed by UHPLC-Q-TOF MS analysis. Pareto-scaled principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis were performed. In Cohort 1, the mPFS and mOS of long-survival patients are 27.05 and NR months, respectively, and those of short-survival patients are 2.79 and 10.59 months. In Cohort 2, the mPFS and mOS of long-survival patients are 27.35 and NR months, respectively, and those of short-survival patients are 3.77 and 12.17 months. A total of 41 unique metabolites in Cohort 1 and 47 in Cohort 2 were screened. In Cohorts 1 and 2, there are 6 differential metabolites each that are significantly associated with both progression-free survival and overall survival. The AUC values for all groups ranged from 0.73 to 0.95. In cohort 1, the top 3 enriched KEGG pathways, as determined through significant different metabolic pathway analysis, were primary bile acid biosynthesis, African trypanosomiasis, and choline metabolism in cancer. In Cohort 2, the top 3 enriched KEGG pathways were the citrate cycle (TCA cycle), PPAR signaling pathway, and primary bile acid biosynthesis. The primary bile acid synthesis pathway had significant differences in the long-term and short-term survival groups in both Cohorts 1 and 2. Our study suggests that peripheral blood metabolomic analysis is critical for identifying metabolic biomarkers and pathways responsible for the patients with NSCLC treated with ICIs.
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Affiliation(s)
- Yanjun Xu
- Department of Medical Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Kaibo Ding
- Department of Medical Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Zhongsheng Peng
- Department of Medical Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Ling Ding
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hui Li
- Department of Medical Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Yun Fan
- Department of Medical Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
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Mattison DR, Momoli F, Alyanak C, Aschner M, Baker M, Cashman N, Dydak U, Farhat N, Guilarte TR, Karyakina N, Ramoju S, Shilnikova N, Taba P, Krewski D. Diagnosis of manganism and manganese neurotoxicity: A workshop report. MEDICINE INTERNATIONAL 2024; 4:11. [PMID: 38410758 PMCID: PMC10895461 DOI: 10.3892/mi.2024.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
With declining exposures to manganese (Mn) in occupational settings, there is a need for more sensitive exposure assessments and clinical diagnostic criteria for manganism and Mn neurotoxicity. To address this issue, a workshop was held on November 12-13, 2020, with international experts on Mn toxicity. The workshop discussions focused on the history of the diagnostic criteria for manganism, including those developed by the Institut de Recherche Robert-Sauvé en Santé et en Sécurité du Travail (IRSST) in Quebec in 2005 and criteria developed by the Chinese government in 2002 and updated in 2006; the utility of biomarkers of exposure; recent developments in magnetic resonance imaging (MRI) for assessing Mn accumulation in the brain and diagnosing manganism; and potential future applications of metabolomics. The suggestions of the participants for updating manganism diagnostic criteria included the consideration of: i) A history of previous occupational and environmental exposure to Mn; ii) relevant clinical symptoms such as dystonia; iii) MRI imaging to document Mn accumulation in the neural tissues, including the basal ganglia; and iv) criteria for the differential diagnosis of manganism and other neurological conditions. Important research gaps include the characterization of Mn exposure and other co-exposures, exploration of the roles of different brain regions with MRI, understanding the complexity of metal ion transporters involved in Mn homeostasis, and a need for information on other neurotransmitter systems and brain regions underlying the pathophysiology of manganism.
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Affiliation(s)
- Donald R. Mattison
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
- Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Franco Momoli
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
| | - Cemil Alyanak
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Marissa Baker
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Neil Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- ProMIS Neurosciences, Inc., Toronto, ON M4S 3E2, Canada
| | - Ulrike Dydak
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Nawal Farhat
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
| | - Tomás R. Guilarte
- Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL 33199, USA
| | | | - Siva Ramoju
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
| | - Natalia Shilnikova
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
- R. Samuel McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
| | - Pille Taba
- Department of Neurology and Neurosurgery, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
- Neurology Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Daniel Krewski
- Risk Sciences International, Ottawa, ON K1P 5J6, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
- R. Samuel McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
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Fall F, Mamede L, Vast M, De Tullio P, Hayette MP, Michels PAM, Frédérich M, Govaerts B, Quetin-Leclercq J. First comprehensive untargeted metabolomics study of suramin-treated Trypanosoma brucei: an integrated data analysis workflow from multifactor data modelling to functional analysis. Metabolomics 2024; 20:25. [PMID: 38393408 DOI: 10.1007/s11306-024-02094-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
INTRODUCTION Human African trypanosomiasis, commonly known as sleeping sickness, is a vector-borne parasitic disease prevalent in sub-Saharan Africa and transmitted by the tsetse fly. Suramin, a medication with a long history of clinical use, has demonstrated varied modes of action against Trypanosoma brucei. This study employs a comprehensive workflow to investigate the metabolic effects of suramin on T. brucei, utilizing a multimodal metabolomics approach. OBJECTIVES The primary aim of this study is to comprehensively analyze the metabolic impact of suramin on T. brucei using a combined liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance spectroscopy (NMR) approach. Statistical analyses, encompassing multivariate analysis and pathway enrichment analysis, are applied to elucidate significant variations and metabolic changes resulting from suramin treatment. METHODS A detailed methodology involving the integration of high-resolution data from LC-MS and NMR techniques is presented. The study conducts a thorough analysis of metabolite profiles in both suramin-treated and control T. brucei brucei samples. Statistical techniques, including ANOVA-simultaneous component analysis (ASCA), principal component analysis (PCA), ANOVA 2 analysis, and bootstrap tests, are employed to discern the effects of suramin treatment on the metabolomics outcomes. RESULTS Our investigation reveals substantial differences in metabolic profiles between the control and suramin-treated groups. ASCA and PCA analysis confirm distinct separation between these groups in both MS-negative and NMR analyses. Furthermore, ANOVA 2 analysis and bootstrap tests confirmed the significance of treatment, time, and interaction effects on the metabolomics outcomes. Functional analysis of the data from LC-MS highlighted the impact of treatment on amino-acid, and amino-sugar and nucleotide-sugar metabolism, while time effects were observed on carbon intermediary metabolism (notably glycolysis and di- and tricarboxylic acids of the succinate production pathway and tricarboxylic acid (TCA) cycle). CONCLUSION Through the integration of LC-MS and NMR techniques coupled with advanced statistical analyses, this study identifies distinctive metabolic signatures and pathways associated with suramin treatment in T. brucei. These findings contribute to a deeper understanding of the pharmacological impact of suramin and have the potential to inform the development of more efficacious therapeutic strategies against African trypanosomiasis.
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Affiliation(s)
- Fanta Fall
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier, B1 72.03, 1200, Brussels, Belgium.
| | - Lucia Mamede
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Madeline Vast
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA/LIDAM), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Pascal De Tullio
- Clinical Metabolomics Group (CliMe), Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Marie-Pierre Hayette
- Department of Clinical Microbiology, Centre Hospitalier Universitaire de Liège, Domaine Universitaire, 4000, Liège, Belgium
| | - Paul A M Michels
- School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Bernadette Govaerts
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA/LIDAM), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier, B1 72.03, 1200, Brussels, Belgium
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Quantitative challenges and their bioinformatic solutions in mass spectrometry-based metabolomics. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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Zhang L, Zheng J, Ismond KP, MacKay S, LeVatte M, Constable J, Alatise OI, Kingham TP, Wishart DS. Identification of urinary biomarkers of colorectal cancer: Towards the development of a colorectal screening test in limited resource settings. Cancer Biomark 2023; 36:17-30. [PMID: 35871322 PMCID: PMC10627333 DOI: 10.3233/cbm-220034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND African colorectal cancer (CRC) rates are rising rapidly. A low-cost CRC screening approach is needed to identify CRC from non-CRC patients who should be sent for colonoscopy (a scarcity in Africa). OBJECTIVE To identify urinary metabolite biomarkers that, combined with easy-to-measure clinical variables, would identify patients that should be further screened for CRC by colonoscopy. Ideal metabolites would be water-soluble and easily translated into a sensitive, low-cost point-of-care (POC) test. METHODS Liquid-chromatography mass spectrometry (LC-MS/MS) was used to quantify 142 metabolites in spot urine samples from 514 Nigerian CRC patients and healthy controls. Metabolite concentration data and clinical characteristics were used to determine optimal sets of biomarkers for identifying CRC from non-CRC subjects. RESULTS Our statistical analysis identified N1, N12-diacetylspermine, hippurate, p-hydroxyhippurate, and glutamate as the best metabolites to discriminate CRC patients via POC screening. Logistic regression modeling using these metabolites plus clinical data achieved an area under the receiver-operator characteristic (AUCs) curves of 89.2% for the discovery set, and 89.7% for a separate validation set. CONCLUSIONS Effective urinary biomarkers for CRC screening do exist. These results could be transferred into a simple, POC urinary test for screening CRC patients in Africa.
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Affiliation(s)
- Lun Zhang
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jiamin Zheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Scott MacKay
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcia LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jeremy Constable
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olusegun Isaac Alatise
- Department of Surgery, Obafemi Awolowo University and Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - T. Peter Kingham
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Póvoa P, Bos LDJ, Coelho L. The role of proteomics and metabolomics in severe infections. Curr Opin Crit Care 2022; 28:534-539. [PMID: 35942690 DOI: 10.1097/mcc.0000000000000966] [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: 11/25/2022]
Abstract
PURPOSE OF REVIEW Severe infections are a common cause of ICU admission, with a high morbidity and mortality. Omics, namely proteomics and metabolomics, aim to identify, characterize, and quantify biological molecules to achieve a systems-level understanding of disease. The aim of this review is to provide a clear overview of the current evidence of the role of proteomics and metabolomics in severe infections. RECENT FINDINGS Proteomics and metabolomics are technologies that are being used to explore new markers of diagnosis and prognosis, clarify mechanisms of disease, and consequently discover potential targets of therapy and finally of a better disease phenotyping. These technologies are starting to be used but not yet in clinical use. SUMMARY Our traditional way of approaching the disease as sepsis is believing that a process can be broken into its parts and that the whole can be explained by the sum of each part. This approach is highly reductionist and does not take the system complexity nor the nonlinear dynamics of the processes. Proteomics and metabolomics allow the analysis of several proteins and metabolites simultaneously, thereby generating diagnostic and prognostic signatures. An exciting future prospect for proteomics and metabolomics is their employment towards precision medicine.
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Affiliation(s)
- Pedro Póvoa
- NOVA Medical School, CHRC, New University of Lisbon
- Polyvalent Intensive Care Unit, Hospital de São Francisco Xavier, CHLO, Lisbon, Portugal
- Center for Clinical Epidemiology and Research Unit of Clinical Epidemiology, OUH Odense University Hospital, Odense, Denmark
| | - Lieuwe D J Bos
- Intensive Care, Infection and Immunity
- Department of Respiratory Medicine, Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Luís Coelho
- NOVA Medical School, CHRC, New University of Lisbon
- Polyvalent Intensive Care Unit, Hospital de São Francisco Xavier, CHLO, Lisbon, Portugal
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Feng K, Dai W, Liu L, Li S, Gou Y, Chen Z, Chen G, Fu X. Identification of biomarkers and the mechanisms of multiple trauma complicated with sepsis using metabolomics. Front Public Health 2022; 10:923170. [PMID: 35991069 PMCID: PMC9387941 DOI: 10.3389/fpubh.2022.923170] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
Sepsis after trauma increases the risk of mortality rate for patients in intensive care unit (ICUs). Currently, it is difficult to predict outcomes in individual patients with sepsis due to the complexity of causative pathogens and the lack of specific treatment. This study aimed to identify metabolomic biomarkers in patients with multiple trauma and those with multiple trauma accompanied with sepsis. Therefore, the metabolic profiles of healthy persons designated as normal controls (NC), multiple trauma patients (MT), and multiple trauma complicated with sepsis (MTS) (30 cases in each group) were analyzed with ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS)-based untargeted plasma metabolomics using collected plasma samples. The differential metabolites were enriched in amino acid metabolism, lipid metabolism, glycometabolism and nucleotide metabolism. Then, nine potential biomarkers, namely, acrylic acid, 5-amino-3-oxohexanoate, 3b-hydroxy-5-cholenoic acid, cytidine, succinic acid semialdehyde, PE [P-18:1(9Z)/16:1(9Z)], sphinganine, uracil, and uridine, were found to be correlated with clinical variables and validated using receiver operating characteristic (ROC) curves. Finally, the three potential biomarkers succinic acid semialdehyde, uracil and uridine were validated and can be applied in the clinical diagnosis of multiple traumas complicated with sepsis.
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Affiliation(s)
- Ke Feng
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Wenjie Dai
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Ling Liu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Shengming Li
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yi Gou
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Zhongwei Chen
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Guodong Chen
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
- *Correspondence: Guodong Chen
| | - Xufeng Fu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
- Xufeng Fu
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Urinary Metabolomic Profile of Neonates Born to Women with Gestational Diabetes Mellitus. Metabolites 2021; 11:metabo11110723. [PMID: 34822382 PMCID: PMC8621167 DOI: 10.3390/metabo11110723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is one of the most frequent pregnancy complications with potential adverse outcomes for mothers and newborns. Its effects on the newborn appear during the neonatal period or early childhood. Therefore, an early diagnosis is crucial to prevent the development of chronic diseases later in adult life. In this study, the urinary metabolome of babies born to GDM mothers was characterized. In total, 144 neonatal and maternal (second and third trimesters of pregnancy) urinary samples were analyzed using targeted metabolomics, combining liquid chromatographic mass spectrometry (LC-MS/MS) and flow injection analysis mass spectrometry (FIA-MS/MS) techniques. We provide here the neonatal urinary concentration values of 101 metabolites for 26 newborns born to GDM mothers and 22 newborns born to healthy mothers. The univariate analysis of these metabolites revealed statistical differences in 11 metabolites. Multivariate analyses revealed a differential metabolic profile in newborns of GDM mothers characterized by dysregulation of acylcarnitines, amino acids, and polyamine metabolism. Levels of hexadecenoylcarnitine (C16:1) and spermine were also higher in newborns of GDM mothers. The maternal urinary metabolome revealed significant differences in butyric, isobutyric, and uric acid in the second and third trimesters of pregnancy. These metabolic alterations point to the impact of GDM in the neonatal period.
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Qi SA, Wu Q, Chen Z, Zhang W, Zhou Y, Mao K, Li J, Li Y, Chen J, Huang Y, Huang Y. High-resolution metabolomic biomarkers for lung cancer diagnosis and prognosis. Sci Rep 2021; 11:11805. [PMID: 34083687 PMCID: PMC8175557 DOI: 10.1038/s41598-021-91276-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the leading cause of human cancer mortality due to the lack of early diagnosis technology. The low-dose computed tomography scan (LDCT) is one of the main techniques to screen cancers. However, LDCT still has a risk of radiation exposure and it is not suitable for the general public. In this study, plasma metabolic profiles of lung cancer were performed using a comprehensive metabolomic method with different liquid chromatography methods coupled with a Q-Exactive high-resolution mass spectrometer. Metabolites with different polarities (amino acids, fatty acids, and acylcarnitines) can be detected and identified as differential metabolites of lung cancer in small volumes of plasma. Logistic regression models were further developed to identify cancer stages and types using those significant biomarkers. Using the Variable Importance in Projection (VIP) and the area under the curve (AUC) scores, we have successfully identified the top 5, 10, and 20 metabolites that can be used to differentiate lung cancer stages and types. The discrimination accuracy and AUC score can be as high as 0.829 and 0.869 using the five most significant metabolites. This study demonstrated that using 5 + metabolites (Palmitic acid, Heptadecanoic acid, 4-Oxoproline, Tridecanoic acid, Ornithine, and etc.) has the potential for early lung cancer screening. This finding is useful for transferring the diagnostic technology onto a point-of-care device for lung cancer diagnosis and prognosis.
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Affiliation(s)
- Shi-Ang Qi
- Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, 650118, Yunnan, China
| | - Qian Wu
- Shanghai Center for Bioinformation Technology and Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai, 201203, China
- Shanghai Fenglin Clinical Laboratory Co., Ltd, Shanghai, 200231, China
| | - Zhenpu Chen
- Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, 650118, Yunnan, China
| | - Wei Zhang
- Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Yongchun Zhou
- Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, 650118, Yunnan, China
| | - Kaining Mao
- Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Jia Li
- Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, 650118, Yunnan, China
| | - Yuanyuan Li
- Shanghai Center for Bioinformation Technology and Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai, 201203, China
| | - Jie Chen
- Electrical and Computer Engineering, University of Alberta, Edmonton, Canada.
| | - Youguang Huang
- Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, 650118, Yunnan, China.
| | - Yunchao Huang
- Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, 650118, Yunnan, China.
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Friedman P, Yilmaz A, Ugur Z, Jafar F, Whitten A, Ustun I, Turkoglu O, Graham S, Bahado Singh R. Urine metabolomic biomarkers for prediction of isolated fetal congenital heart defect. J Matern Fetal Neonatal Med 2021; 35:6380-6387. [PMID: 33944672 DOI: 10.1080/14767058.2021.1914572] [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: 10/21/2022]
Abstract
OBJECTIVE To identify maternal second and third trimester urine metabolomic biomarkers for the detection of fetal congenital heart defects (CHDs). STUDY DESIGN This was a prospective study. Metabolomic analysis of randomly collected maternal urine was performed, comparing pregnancies with isolated, non-syndromic CHDs versus unaffected controls. Mass spectrometry (liquid chromatography and direct injection and tandem mass spectrometry, LC-MS-MS) as well as nuclear magnetic resonance spectrometry, 1H NMR, were used to perform the analyses between 14 0/7 and 37 0/7 weeks gestation. A total of 36 CHD cases and 41 controls were compared. Predictive algorithms using urine markers alone or combined with, clinical and ultrasound (US) (four-chamber view) predictors were developed and compared. RESULTS A total of 222 metabolites were identified, of which 16 were overlapping between the two platforms. Twenty-three metabolite concentrations were found in significantly altered in CHD gestations on univariate analysis. The concentration of methionine was most significantly altered. A predictive algorithm combining metabolites (histamine, choline, glucose, formate, methionine, and carnitine) plus US four-chamber view achieved an AUC = 0.894; 95% CI, 0814-0.973 with a sensitivity of 83.8% and specificity of 87.8%. Enrichment pathway analysis identified several lipid related pathways that are dysregulated in CHD, including phospholipid biosynthesis, phosphatidylcholine biosynthesis, phosphatidylethanolamine biosynthesis, and fatty acid metabolism. This could be consistent with the increased risk of CHD in diabetic pregnancies. CONCLUSIONS We report a novel, noninvasive approach, based on the analysis of maternal urine for isolated CHD detection. Further, the dysregulation of lipid- and folate metabolism appears to support prior data on the mechanism of CHD.
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Affiliation(s)
- Perry Friedman
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Ali Yilmaz
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Zafer Ugur
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Faryal Jafar
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Amy Whitten
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Ilyas Ustun
- Center for Data Science,DePaul University School of Computing, Chicago, IL, USA
| | - Onur Turkoglu
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Stewart Graham
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
| | - Ray Bahado Singh
- Division of Maternal Fetal Medicine, William Beaumont Health, Royal Oak, MI, USA
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Robust Metabolite Quantification from J-Compensated 2D 1H- 13C-HSQC Experiments. Metabolites 2020; 10:metabo10110449. [PMID: 33171777 PMCID: PMC7695005 DOI: 10.3390/metabo10110449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 02/05/2023] Open
Abstract
The spectral resolution of 2D 1H-13C heteronuclear single quantum coherence (1H-13C-HSQC) nuclear magnetic resonance (NMR) spectra facilitates both metabolite identification and quantification in nuclear magnetic resonance-based metabolomics. However, quantification is complicated by variations in magnetization transfer, which among others originate mainly from scalar coupling differences. Methods that compensate for variation in scalar coupling include the generation of calibration factors for individual signals or the use of additional pulse sequence schemes such as quantitative HSQC (Q-HSQC) that suppress the JCH-dependence by modulating the polarization transfer delays of HSQC or, additionally, employ a pure-shift homodecoupling approach in the 1H dimension, such as Quantitative, Perfected and Pure Shifted HSQC (QUIPU-HSQC). To test the quantitative accuracy of these three methods, employing a 600 MHz NMR spectrometer equipped with a helium cooled cryoprobe, a Latin-square design that covered the physiological concentration ranges of 10 metabolites was used. The results show the suitability of all three methods for the quantification of highly abundant metabolites. However, the substantially increased residual water signal observed in QUIPU-HSQC spectra impeded the quantification of low abundant metabolites located near the residual water signal, thus limiting its utility in high-throughput metabolite fingerprinting studies.
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Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060831] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.
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Graham SF, Turkoglu O, Yilmaz A, Ustun I, Ugur Z, Bjorndhal T, Han B, Mandal R, Wishart D, Bahado-Singh RO. Targeted metabolomics highlights perturbed metabolism in the brain of autism spectrum disorder sufferers. Metabolomics 2020; 16:59. [PMID: 32333121 DOI: 10.1007/s11306-020-01685-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by deficiencies in social interactions and communication, combined with restricted and repetitive behavioral issues. OBJECTIVES As little is known about the etiopathophysiology of ASD and early diagnosis is relatively subjective, we aim to employ a targeted, fully quantitative metabolomics approach to biochemically profile post-mortem human brain with the overall goal of identifying metabolic pathways that may have been perturbed as a result of the disease while uncovering potential central diagnostic biomarkers. METHODS Using a combination of 1H NMR and DI/LC-MS/MS we quantitatively profiled the metabolome of the posterolateral cerebellum from post-mortem human brain harvested from people who suffered with ASD (n = 11) and compared them with age-matched controls (n = 10). RESULTS We accurately identified and quantified 203 metabolites in post-mortem brain extracts and performed a metabolite set enrichment analyses identifying 3 metabolic pathways as significantly perturbed (p < 0.05). These include Pyrimidine, Ubiquinone and Vitamin K metabolism. Further, using a variety of machine-based learning algorithms, we identified a panel of central biomarkers (9-hexadecenoylcarnitine (C16:1) and the phosphatidylcholine PC ae C36:1) capable of discriminating between ASD and controls with an AUC = 0.855 with a sensitivity and specificity equal to 0.80 and 0.818, respectively. CONCLUSION For the first time, we report the use of a multi-platform metabolomics approach to biochemically profile brain from people with ASD and report several metabolic pathways which are perturbed in the diseased brain of ASD sufferers. Further, we identified a panel of biomarkers capable of distinguishing ASD from control brains. We believe that these central biomarkers may be useful for diagnosing ASD in more accessible biomatrices.
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Affiliation(s)
- Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA.
- Research Institute, Metabolomics Division, Beaumont Health, Royal Oak, MI, 48073, USA.
| | - Onur Turkoglu
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
| | - Ali Yilmaz
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Research Institute, Metabolomics Division, Beaumont Health, Royal Oak, MI, 48073, USA
| | - Ilyas Ustun
- Wayne State University, Civil and Environmental Engineering, Detroit, MI, USA
| | - Zafer Ugur
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Research Institute, Metabolomics Division, Beaumont Health, Royal Oak, MI, 48073, USA
| | - Trent Bjorndhal
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - BeomSoo Han
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rupa Mandal
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - David Wishart
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ray O Bahado-Singh
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
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Zhang L, Zheng J, Ahmed R, Huang G, Reid J, Mandal R, Maksymuik A, Sitar DS, Tappia PS, Ramjiawan B, Joubert P, Russo A, Rolfo CD, Wishart DS. A High-Performing Plasma Metabolite Panel for Early-Stage Lung Cancer Detection. Cancers (Basel) 2020; 12:cancers12030622. [PMID: 32156060 PMCID: PMC7139410 DOI: 10.3390/cancers12030622] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
The objective of this research is to use metabolomic techniques to discover and validate plasma metabolite biomarkers for the diagnosis of early-stage non-small cell lung cancer (NSCLC). The study included plasma samples from 156 patients with biopsy-confirmed NSCLC along with age and gender-matched plasma samples from 60 healthy controls. A fully quantitative targeted mass spectrometry (MS) analysis (targeting 138 metabolites) was performed on all samples. The sample set was split into a discovery set and validation set. Metabolite concentration data, clinical data, and smoking history were used to determine optimal sets of biomarkers and optimal regression models for identifying different stages of NSCLC using the discovery sets. The same biomarkers and regression models were used and assessed on the validation models. Univariate and multivariate statistical analysis identified β-hydroxybutyric acid, LysoPC 20:3, PC ae C40:6, citric acid, and fumaric acid as being significantly different between healthy controls and stage I/II NSCLC. Robust predictive models with areas under the curve (AUC) > 0.9 were developed and validated using these metabolites and other, easily measured clinical data for detecting different stages of NSCLC. This study successfully identified and validated a simple, high-performing, metabolite-based test for detecting early stage (I/II) NSCLC patients in plasma. While promising, further validation on larger and more diverse cohorts is still required.
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Affiliation(s)
- Lun Zhang
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Jiamin Zheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Rashid Ahmed
- BioMark Diagnostics Inc., Richmond, BC V6X 2W8, Canada; (R.A.); (G.H.)
| | - Guoyu Huang
- BioMark Diagnostics Inc., Richmond, BC V6X 2W8, Canada; (R.A.); (G.H.)
| | - Jennifer Reid
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Andrew Maksymuik
- Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1R9, Canada;
| | - Daniel S. Sitar
- Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1R9, Canada;
- Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Paramjit S. Tappia
- Asper Clinical Research Institute & Office of Clinical Research, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada; (P.S.T.); (B.R.)
| | - Bram Ramjiawan
- Asper Clinical Research Institute & Office of Clinical Research, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada; (P.S.T.); (B.R.)
| | - Philippe Joubert
- Department of Pathology, University of Laval, Quebec, QC G1V 4G5, Canada;
| | - Alessandro Russo
- Medical Oncology Unit A.O. Papardo & Department of Human Pathology, University of Messina, 98158 Messina, Italy;
- Thoracic Medical Oncology Program Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA;
| | - Christian D. Rolfo
- Thoracic Medical Oncology Program Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA;
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
- Correspondence:
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Wishart DS. Metabolomics for Investigating Physiological and Pathophysiological Processes. Physiol Rev 2019; 99:1819-1875. [PMID: 31434538 DOI: 10.1152/physrev.00035.2018] [Citation(s) in RCA: 472] [Impact Index Per Article: 94.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry techniques to enable the high-throughput characterization of metabolites from cells, organs, tissues, or biofluids. The rapid growth in metabolomics is leading to a renewed interest in metabolism and the role that small molecule metabolites play in many biological processes. As a result, traditional views of metabolites as being simply the "bricks and mortar" of cells or just the fuel for cellular energetics are being upended. Indeed, metabolites appear to have much more varied and far more important roles as signaling molecules, immune modulators, endogenous toxins, and environmental sensors. This review explores how metabolomics is yielding important new insights into a number of important biological and physiological processes. In particular, a major focus is on illustrating how metabolomics and discoveries made through metabolomics are improving our understanding of both normal physiology and the pathophysiology of many diseases. These discoveries are yielding new insights into how metabolites influence organ function, immune function, nutrient sensing, and gut physiology. Collectively, this work is leading to a much more unified and system-wide perspective of biology wherein metabolites, proteins, and genes are understood to interact synergistically to modify the actions and functions of organelles, organs, and organisms.
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Affiliation(s)
- David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
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Bahado-Singh RO, Sonek J, McKenna D, Cool D, Aydas B, Turkoglu O, Bjorndahl T, Mandal R, Wishart D, Friedman P, Graham SF, Yilmaz A. Artificial intelligence and amniotic fluid multiomics: prediction of perinatal outcome in asymptomatic women with short cervix. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 54:110-118. [PMID: 30381856 DOI: 10.1002/uog.20168] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To evaluate the application of artificial intelligence (AI), i.e. deep learning and other machine-learning techniques, to amniotic fluid (AF) metabolomics and proteomics, alone and in combination with sonographic, clinical and demographic factors, in the prediction of perinatal outcome in asymptomatic pregnant women with short cervical length (CL). METHODS AF samples, which had been obtained in the second trimester from asymptomatic women with short CL (< 15 mm) identified on transvaginal ultrasound, were analyzed. CL, funneling and the presence of AF 'sludge' were assessed in all cases close to the time of amniocentesis. A combination of liquid chromatography coupled with mass spectrometry and proton nuclear magnetic resonance spectroscopy-based metabolomics, as well as targeted proteomics analysis, including chemokines, cytokines and growth factors, was performed on the AF samples. To determine the robustness of the markers, we used six different machine-learning techniques, including deep learning, to predict preterm delivery < 34 weeks, latency period prior to delivery < 28 days after amniocentesis and requirement for admission to a neonatal intensive care unit (NICU). Omics biomarkers were evaluated alone and in combination with standard sonographic, clinical and demographic factors to predict outcome. Predictive accuracy was assessed using the area under the receiver-operating characteristics curve (AUC) with 95% CI, sensitivity and specificity. RESULTS Of the 32 patients included in the study, complete omics, demographic and clinical data and outcome information were available for 26. Of these, 11 (42.3%) patients delivered ≥ 34 weeks, while 15 (57.7%) delivered < 34 weeks. There was no statistically significant difference in CL between these two groups (mean ± SD, 11.2 ± 4.4 mm vs 8.9 ± 5.3 mm, P = 0.31). Using combined omics, demographic and clinical data, deep learning displayed good to excellent performance, with an AUC (95% CI) of 0.890 (0.810-0.970) for delivery < 34 weeks' gestation, 0.890 (0.790-0.990) for delivery < 28 days post-amniocentesis and 0.792 (0.689-0.894) for NICU admission. These values were higher overall than for the other five machine-learning methods, although each individual machine-learning technique yielded statistically significant prediction of the different perinatal outcomes. CONCLUSIONS This is the first study to report use of AI with AF proteomics and metabolomics and ultrasound assessment in pregnancy. Machine learning, particularly deep learning, achieved good to excellent prediction of perinatal outcome in asymptomatic pregnant women with short CL in the second trimester. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- R O Bahado-Singh
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, USA
| | - J Sonek
- Division of Maternal Fetal Medicine, Wright State University, Dayton, OH, USA
| | - D McKenna
- Department of Obstetrics and Gynecology, Miami Valley Hospital South, Tampa, FL, USA
| | - D Cool
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, USA
| | - B Aydas
- Department of Computer Science, Albion College, Albion, MI, USA
| | - O Turkoglu
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, USA
| | - T Bjorndahl
- Department of Biological Science, University of Alberta, Edmonton, AB, Canada
| | - R Mandal
- Department of Biological Science, University of Alberta, Edmonton, AB, Canada
| | - D Wishart
- Department of Biological Science, University of Alberta, Edmonton, AB, Canada
| | - P Friedman
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, USA
| | - S F Graham
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, USA
| | - A Yilmaz
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, USA
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19
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Bayci AWL, Baker DA, Somerset AE, Turkoglu O, Hothem Z, Callahan RE, Mandal R, Han B, Bjorndahl T, Wishart D, Bahado-Singh R, Graham SF, Keidan R. Metabolomic identification of diagnostic serum-based biomarkers for advanced stage melanoma. Metabolomics 2018; 14:105. [PMID: 30830422 DOI: 10.1007/s11306-018-1398-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/18/2018] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Melanoma is a highly aggressive malignancy and is currently one of the fastest growing cancers worldwide. While early stage (I and II) disease is highly curable with excellent prognosis, mortality rates rise dramatically after distant spread. We sought to identify differences in the metabolome of melanoma patients to further elucidate the pathophysiology of melanoma and identify potential biomarkers to aid in earlier detection of recurrence. METHODS Using 1H NMR and DI-LC-MS/MS, we profiled serum samples from 26 patients with stage III (nodal metastasis) or stage IV (distant metastasis) melanoma and compared their biochemical profiles with 46 age- and gender-matched controls. RESULTS We accurately quantified 181 metabolites in serum using a combination of 1H NMR and DI-LC-MS/MS. We observed significant separation between cases and controls in the PLS-DA scores plot (permutation test p-value = 0.002). Using the concentrations of PC-aa-C40:3, DL-carnitine, octanoyl-L-carnitine, ethanol, and methylmalonyl-L-carnitine we developed a diagnostic algorithm with an AUC (95% CI) = 0.822 (0.665-0.979) with sensitivity and specificity of 100 and 56%, respectively. Furthermore, we identified arginine, proline, tryptophan, glutamine, glutamate, glutathione and ornithine metabolism to be significantly perturbed due to disease (p < 0.05). CONCLUSION Targeted metabolomic analysis demonstrated significant differences in metabolic profiles of advanced stage (III and IV) melanoma patients as compared to controls. These differences may represent a potential avenue for the development of multi-marker serum-based assays for earlier detection of recurrences, allow for newer, more effective targeted therapy when tumor burden is less, and further elucidate the pathophysiologic changes that occur in melanoma.
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Affiliation(s)
- A W L Bayci
- Department of General Surgery, Beaumont Health, Royal Oak, MI, USA
| | - D A Baker
- Department of General Surgery, Beaumont Health, Royal Oak, MI, USA.
- Department of Surgery, Beaumont Health, 3601 W. 13 Mile Rd., Royal Oak, MI, 48073, USA.
| | - A E Somerset
- Department of General Surgery, Beaumont Health, Royal Oak, MI, USA
| | - O Turkoglu
- Department of Obstetrics and Gynecology, Beaumont Health, Royal Oak, MI, USA
| | - Z Hothem
- Department of General Surgery, Beaumont Health, Royal Oak, MI, USA
| | - R E Callahan
- Department of General Surgery, Beaumont Health, Royal Oak, MI, USA
| | - R Mandal
- Department of Biological and Computing Sciences, University of Alberta Edmonton, Edmonton, AB, Canada
| | - B Han
- Department of Biological and Computing Sciences, University of Alberta Edmonton, Edmonton, AB, Canada
| | - T Bjorndahl
- Department of Biological and Computing Sciences, University of Alberta Edmonton, Edmonton, AB, Canada
| | - D Wishart
- Department of Biological and Computing Sciences, University of Alberta Edmonton, Edmonton, AB, Canada
| | - R Bahado-Singh
- Department of Obstetrics and Gynecology, Beaumont Health, Royal Oak, MI, USA
| | - S F Graham
- Department of Obstetrics and Gynecology, Beaumont Health, Royal Oak, MI, USA
| | - R Keidan
- Department of General Surgery, Beaumont Health, Royal Oak, MI, USA
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Targeted biochemical profiling of brain from Huntington's disease patients reveals novel metabolic pathways of interest. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2430-2437. [DOI: 10.1016/j.bbadis.2018.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/28/2018] [Accepted: 04/17/2018] [Indexed: 12/14/2022]
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Evangelatos N, Bauer P, Reumann M, Satyamoorthy K, Lehrach H, Brand A. Metabolomics in Sepsis and Its Impact on Public Health. Public Health Genomics 2018; 20:274-285. [PMID: 29353273 DOI: 10.1159/000486362] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/16/2017] [Indexed: 12/11/2022] Open
Abstract
Sepsis, with its often devastating consequences for patients and their families, remains a major public health concern that poses an increasing financial burden. Early resuscitation together with the elucidation of the biological pathways and pathophysiological mechanisms with the use of "-omics" technologies have started changing the clinical and research landscape in sepsis. Metabolomics (i.e., the study of the metabolome), an "-omics" technology further down in the "-omics" cascade between the genome and the phenome, could be particularly fruitful in sepsis research with the potential to alter the clinical practice. Apart from its benefit for the individual patient, metabolomics has an impact on public health that extends beyond its applications in medicine. In this review, we present recent developments in metabolomics research in sepsis, with a focus on pneumonia, and we discuss the impact of metabolomics on public health, with a focus on free/libre open source software.
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Affiliation(s)
- Nikolaos Evangelatos
- Intensive Care Medicine Unit, Department of Respiratory Medicine, Allergology and Sleep Medicine, Paracelsus Medical University, Nuremberg, Germany.,UNU-MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Maastricht, the Netherlands
| | - Pia Bauer
- Intensive Care Medicine Unit, Department of Respiratory Medicine, Allergology and Sleep Medicine, Paracelsus Medical University, Nuremberg, Germany
| | - Matthias Reumann
- UNU-MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Maastricht, the Netherlands.,IBM Research - Zurich, Rueschlikon, Switzerland
| | | | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Angela Brand
- UNU-MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Maastricht, the Netherlands.,Public Health Genomics, Department of International Health, Maastricht University, Maastricht, the Netherlands.,Manipal University, Madhav Nagar, Manipal, India
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Ebbels TMD, Rodriguez-Martinez A, Dumas ME, Keun HC. Advances in Computational Analysis of Metabolomic NMR Data. NMR-BASED METABOLOMICS 2018. [DOI: 10.1039/9781782627937-00310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter we discuss some of the more recent developments in preprocessing and statistical analysis of NMR spectra in metabolomics. Bayesian methods for analyzing NMR spectra are summarized and we describe one particular approach, BATMAN, in more detail. We consider techniques based on statistical associations, such as correlation spectroscopy (e.g. STOCSY and recent variants), as well as approaches that model the associations as a network and how these change under different biological conditions. The link between metabolism and genotype is explored by looking at metabolic GWAS and related techniques. Finally, we describe the relevance and current status of data standards for NMR metabolomics.
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Affiliation(s)
- Timothy M. D. Ebbels
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London SW7 2AZ UK
| | - Andrea Rodriguez-Martinez
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London SW7 2AZ UK
| | - Marc-Emmanuel Dumas
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London SW7 2AZ UK
| | - Hector C. Keun
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London W12 0NN UK
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Bahado-Singh RO, Lugade A, Field J, Al-Wahab Z, Han B, Mandal R, Bjorndahl TC, Turkoglu O, Graham SF, Wishart D, Odunsi K. Metabolomic prediction of endometrial cancer. Metabolomics 2017; 14:6. [PMID: 30830361 DOI: 10.1007/s11306-017-1290-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Endometrial cancer (EC) is associated with metabolic disturbances including obesity, diabetes and metabolic syndrome. Identifying metabolite biomarkers for EC detection has a crucial role in reducing morbidity and mortality. OBJECTIVE To determine whether metabolomic based biomarkers can detect EC overall and early-stage EC. METHODS We performed NMR and mass spectrometry based metabolomic analyses of serum in EC cases versus controls. A total of 46 early-stage (FIGO stages I-II) and 10 late-stage (FIGO stages III-IV) EC cases constituted the study group. A total of 60 unaffected control samples were used. Patients and controls were divided randomly into a discovery group (n = 69) and an independent validation group (n = 47). Predictive algorithms based on biomarkers and demographic characteristics were generated using logistic regression analysis. RESULTS A total of 181 metabolites were evaluated. Extensive changes in metabolite levels were noted in the EC versus the control group. The combination of C14:2, phosphatidylcholine with acyl-alkyl residue sum C38:1 (PCae C38:1) and 3-hydroxybutyric acid had an area under the receiver operating characteristics curve (AUC) (95% CI) = 0.826 (0.706-0.946) and a sensitivity = 82.6%, and specificity = 70.8% for EC overall. For early EC prediction: BMI, C14:2 and PC ae C40:1 had an AUC (95% CI) = 0.819 (0.689-0.95) and a sensitivity = 72.2% and specificity = 79.2% in the validation group. CONCLUSIONS EC is characterized by significant perturbations in important cellular metabolites. Metabolites accurately detected early-stage EC cases and EC overall which could lead to the development of non-invasive biomarkers for earlier detection of EC and for monitoring disease recurrence.
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Affiliation(s)
- Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, William Beaumont Health, Royal Oak, MI, 48073, USA.
| | - Amit Lugade
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jayson Field
- Department of Gynecologic Oncology, William Beaumont Health, Royal Oak, MI, USA
| | - Zaid Al-Wahab
- Department of Gynecologic Oncology, William Beaumont Health, Royal Oak, MI, USA
| | - BeomSoo Han
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Rupasri Mandal
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Trent C Bjorndahl
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Onur Turkoglu
- Department of Obstetrics and Gynecology, William Beaumont Health, Royal Oak, MI, 48073, USA
| | - Stewart F Graham
- Department of Obstetrics and Gynecology, William Beaumont Health, Royal Oak, MI, 48073, USA
| | - David Wishart
- Departments of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
- Department of Computing Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, USA
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
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Wang H, Muehlbauer MJ, O'Neal SK, Newgard CB, Hauser ER, Bain JR, Shah SH. Recommendations for Improving Identification and Quantification in Non-Targeted, GC-MS-Based Metabolomic Profiling of Human Plasma. Metabolites 2017; 7:E45. [PMID: 28841195 PMCID: PMC5618330 DOI: 10.3390/metabo7030045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Accepted: 08/23/2017] [Indexed: 12/02/2022] Open
Abstract
The field of metabolomics as applied to human disease and health is rapidly expanding. In recent efforts of metabolomics research, greater emphasis has been placed on quality control and method validation. In this study, we report an experience with quality control and a practical application of method validation. Specifically, we sought to identify and modify steps in gas chromatography-mass spectrometry (GC-MS)-based, non-targeted metabolomic profiling of human plasma that could influence metabolite identification and quantification. Our experimental design included two studies: (1) a limiting-dilution study, which investigated the effects of dilution on analyte identification and quantification; and (2) a concentration-specific study, which compared the optimal plasma extract volume established in the first study with the volume used in the current institutional protocol. We confirmed that contaminants, concentration, repeatability and intermediate precision are major factors influencing metabolite identification and quantification. In addition, we established methods for improved metabolite identification and quantification, which were summarized to provide recommendations for experimental design of GC-MS-based non-targeted profiling of human plasma.
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Affiliation(s)
- Hanghang Wang
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Michael J Muehlbauer
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
| | - Sara K O'Neal
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
| | - Christopher B Newgard
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
| | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
| | - James R Bain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
| | - Svati H Shah
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA.
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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Graham SF, Turkoglu O, Kumar P, Yilmaz A, Bjorndahl TC, Han B, Mandal R, Wishart DS, Bahado-Singh RO. Targeted Metabolic Profiling of Post-Mortem Brain from Infants Who Died from Sudden Infant Death Syndrome. J Proteome Res 2017; 16:2587-2596. [PMID: 28608686 DOI: 10.1021/acs.jproteome.7b00157] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Currently little is known about the underlying pathophysiology associated with SIDS, and no objective biomarkers exist for the accurate identification of those at greatest risk of dying from SIDS. Using targeted metabolomics, we aim to profile the medulla oblongata of infants who have died from SIDS (n = 16) and directly compare their biochemical profile with age matched controls. Combining data acquired using 1H NMR and targeted DI-LC-MS/MS, we have identified fatty acid oxidation as a pivotal biochemical pathway perturbed in the brains of those infants who have from SIDS (p = 0.0016). Further we have identified a potential central biomarker with an AUC (95% CI) = 0.933 (0.845-1.000) having high sensitivity (0.933) and specificity (0.875) values for discriminating between control and SIDS brains. This is the first reported study to use targeted metabolomics for the study of PM brain from infants who have died from SIDS. We have identified pathways associated with the disease and central biomarkers for early screening/diagnosis.
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Affiliation(s)
- Stewart F Graham
- Beaumont Health , 3811 W. 13 Mile Road, Royal Oak, Michigan 48073, United States
| | - Onur Turkoglu
- Beaumont Health , 3811 W. 13 Mile Road, Royal Oak, Michigan 48073, United States
| | - Praveen Kumar
- Beaumont Health , 3811 W. 13 Mile Road, Royal Oak, Michigan 48073, United States
| | - Ali Yilmaz
- Beaumont Health , 3811 W. 13 Mile Road, Royal Oak, Michigan 48073, United States
| | - Trent C Bjorndahl
- Department of Biological and Computing Sciences, University of Alberta , Edmonton, Alberta T6G 2R3, Canada
| | - BeomSoo Han
- Department of Biological and Computing Sciences, University of Alberta , Edmonton, Alberta T6G 2R3, Canada
| | - Rupasri Mandal
- Department of Biological and Computing Sciences, University of Alberta , Edmonton, Alberta T6G 2R3, Canada
| | - David S Wishart
- Department of Biological and Computing Sciences, University of Alberta , Edmonton, Alberta T6G 2R3, Canada
| | - Ray O Bahado-Singh
- Beaumont Health , 3811 W. 13 Mile Road, Royal Oak, Michigan 48073, United States
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Baker MG, Simpson CD, Lin YS, Shireman LM, Seixas N. The Use of Metabolomics to Identify Biological Signatures of Manganese Exposure. Ann Work Expo Health 2017; 61:406-415. [PMID: 28355443 PMCID: PMC6075188 DOI: 10.1093/annweh/wxw032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/06/2016] [Accepted: 12/21/2016] [Indexed: 01/20/2023] Open
Abstract
Objectives Manganese (Mn) is a known neurotoxicant, and given its health effects and ubiquitous nature in metal-working settings, identification of a valid and reproducible biomarker of Mn exposure is of interest. Here, global metabolomics is utilized to determine metabolites that differ between groups defined by Mn exposure status, with the goal being to help inform a potential metabolite biomarker of Mn exposure. Methods Mn exposed subjects were recruited from a Mn steel foundry and Mn unexposed subjects were recruited from crane operators at a metal recycling facility. Over the course of a work day, each subject wore a personal inhalable dust sampler (IOM), and provided an end of shift urine sample that underwent global metabolomics profiling. Both exposed and unexposed subjects were divided into a training set and demographically similar validation set. Using a two-sided adjusted t-test, relative abundances of all metabolites found were compared between Mn exposed and unexposed training sets, and those with a false discovery rates (FDR) <0.1 were further tested in the validation sets. Results Fifteen ions were found to be significantly different (FDR < 0.1) between the exposed and unexposed training sets, and nine of these ions remained significantly different between the exposed and unexposed validation set as well. When further dividing exposure status into 'lower exposure' and 'higher exposure', several of these nine ions exhibited an apparent exposure-response relationship. Conclusions This is the first time that metabolomics has been used to distinguish between Mn exposure status in an occupational cohort, though additional work should be done to replicate these findings with a larger cohort. With metabolite identification by name, empirical formula, or pathway, a better understanding of the relationship between Mn exposure and neurotoxic effects could be elucidated, and a potential metabolite biomarker of Mn exposure could be determined.
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Affiliation(s)
- Marissa G Baker
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Christopher D Simpson
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Yvonne S Lin
- Department of Pharmaceutics, University of Washington, Seattle WA, USA
| | - Laura M Shireman
- Department of Pharmaceutics, University of Washington, Seattle WA, USA
| | - Noah Seixas
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
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Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions. mSphere 2017; 2:mSphere00005-17. [PMID: 28194448 PMCID: PMC5299068 DOI: 10.1128/msphere.00005-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Despite the fundamental importance of antibiotic therapies to human health, their functional impact on the intestinal microbiome and its subsequent ability to recover are poorly understood. Much research in this area has focused on changes in microbiota composition, despite the interdependency and overlapping functions of many members of the microbial community. These relationships make prediction of the functional impact of microbiota-level changes difficult, while analyses based on the metabolome alone provide relatively little insight into the taxon-level changes that underpin changes in metabolite levels. Here, we used combined microbiota and metabolome profiling to characterize changes associated with clinically important antibiotic combinations with distinct effects on the gut. Correlation analysis of changes in the metabolome and microbiota indicate that a combined approach will be essential for a mechanistic understanding of the functional impact of distinct antibiotic classes. The intestinal microbiome plays an essential role in regulating many aspects of host physiology, and its disruption through antibiotic exposure has been implicated in the development of a range of serious pathologies. The complex metabolic relationships that exist between members of the intestinal microbiota and the potential redundancy in functional pathways mean that an integrative analysis of changes in both structure and function are needed to understand the impact of antibiotic exposure. We used a combination of next-generation sequencing and nuclear magnetic resonance (NMR) metabolomics to characterize the effects of two clinically important antibiotic treatments, ciprofloxacin and vancomycin-imipenem, on the intestinal microbiomes of female C57BL/6 mice. This assessment was performed longitudinally and encompassed both antibiotic challenge and subsequent microbiome reestablishment. Both antibiotic treatments significantly altered the microbiota and metabolite compositions of fecal pellets during challenge and recovery. Spearman’s correlation analysis of microbiota and NMR data revealed that, while some metabolites could be correlated with individual operational taxonomic units (OTUs), frequently multiple OTUs were associated with a significant change in a given metabolite. Furthermore, one metabolite, arginine, can be associated with increases/decreases in different sets of OTUs under differing conditions. Taken together, these findings indicate that reliance on shifts in one data set alone will generate an incomplete picture of the functional effect of antibiotic intervention. A full mechanistic understanding will require knowledge of the baseline microbiota composition, combined with both a comparison and an integration of microbiota, metabolomics, and phenotypic data. IMPORTANCE Despite the fundamental importance of antibiotic therapies to human health, their functional impact on the intestinal microbiome and its subsequent ability to recover are poorly understood. Much research in this area has focused on changes in microbiota composition, despite the interdependency and overlapping functions of many members of the microbial community. These relationships make prediction of the functional impact of microbiota-level changes difficult, while analyses based on the metabolome alone provide relatively little insight into the taxon-level changes that underpin changes in metabolite levels. Here, we used combined microbiota and metabolome profiling to characterize changes associated with clinically important antibiotic combinations with distinct effects on the gut. Correlation analysis of changes in the metabolome and microbiota indicate that a combined approach will be essential for a mechanistic understanding of the functional impact of distinct antibiotic classes.
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Metabolic signatures of Huntington's disease (HD): 1 H NMR analysis of the polar metabolome in post-mortem human brain. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1675-84. [DOI: 10.1016/j.bbadis.2016.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 12/22/2022]
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Abstract
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language’s usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a “variable,” the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences. Contemporary biology has largely become computational biology, whether it involves applying physical principles to simulate the motion of each atom in a piece of DNA, or using machine learning algorithms to integrate and mine “omics” data across whole cells (or even entire ecosystems). The ability to design algorithms and program computers, even at a novice level, may be the most indispensable skill that a modern researcher can cultivate. As with human languages, computational fluency is developed actively, not passively. This self-contained text, structured as a hybrid primer/tutorial, introduces any biologist—from college freshman to established senior scientist—to basic computing principles (control-flow, recursion, regular expressions, etc.) and the practicalities of programming and software design. We use the Python language because it now pervades virtually every domain of the biosciences, from sequence-based bioinformatics and molecular evolution to phylogenomics, systems biology, structural biology, and beyond. To introduce both coding (in general) and Python (in particular), we guide the reader via concrete examples and exercises. We also supply, as Supplemental Chapters, a few thousand lines of heavily-annotated, freely distributed source code for personal study.
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Affiliation(s)
- Berk Ekmekci
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Charles E. McAnany
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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Stringer KA, McKay RT, Karnovsky A, Quémerais B, Lacy P. Metabolomics and Its Application to Acute Lung Diseases. Front Immunol 2016; 7:44. [PMID: 26973643 PMCID: PMC4770032 DOI: 10.3389/fimmu.2016.00044] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/29/2016] [Indexed: 12/27/2022] Open
Abstract
Metabolomics is a rapidly expanding field of systems biology that is gaining significant attention in many areas of biomedical research. Also known as metabonomics, it comprises the analysis of all small molecules or metabolites that are present within an organism or a specific compartment of the body. Metabolite detection and quantification provide a valuable addition to genomics and proteomics and give unique insights into metabolic changes that occur in tangent to alterations in gene and protein activity that are associated with disease. As a novel approach to understanding disease, metabolomics provides a "snapshot" in time of all metabolites present in a biological sample such as whole blood, plasma, serum, urine, and many other specimens that may be obtained from either patients or experimental models. In this article, we review the burgeoning field of metabolomics in its application to acute lung diseases, specifically pneumonia and acute respiratory disease syndrome (ARDS). We also discuss the potential applications of metabolomics for monitoring exposure to aerosolized environmental toxins. Recent reports have suggested that metabolomics analysis using nuclear magnetic resonance (NMR) and mass spectrometry (MS) approaches may provide clinicians with the opportunity to identify new biomarkers that may predict progression to more severe disease, such as sepsis, which kills many patients each year. In addition, metabolomics may provide more detailed phenotyping of patient heterogeneity, which is needed to achieve the goal of precision medicine. However, although several experimental and clinical metabolomics studies have been conducted assessing the application of the science to acute lung diseases, only incremental progress has been made. Specifically, little is known about the metabolic phenotypes of these illnesses. These data are needed to substantiate metabolomics biomarker credentials so that clinicians can employ them for clinical decision-making and investigators can use them to design clinical trials.
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Affiliation(s)
- Kathleen A. Stringer
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Paige Lacy
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
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Bahado-Singh RO, Syngelaki A, Akolekar R, Mandal R, Bjondahl TC, Han B, Dong E, Bauer S, Alpay-Savasan Z, Graham S, Turkoglu O, Wishart DS, Nicolaides KH. Validation of metabolomic models for prediction of early-onset preeclampsia. Am J Obstet Gynecol 2015; 213:530.e1-530.e10. [PMID: 26116099 DOI: 10.1016/j.ajog.2015.06.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/13/2015] [Accepted: 06/16/2015] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We sought to perform validation studies of previously published and newly derived first-trimester metabolomic algorithms for prediction of early preeclampsia (PE). STUDY DESIGN Nuclear magnetic resonance-based metabolomic analysis was performed on first-trimester serum in 50 women who subsequently developed early PE and in 108 first-trimester controls. Random stratification and allocation was used to divide cases into a discovery group (30 early PE and 65 controls) for generation of the biomarker model(s) and a validation group (20 early PE and 43 controls) to ensure an unbiased assessment of the predictive algorithms. Cross-validation testing on the different algorithms was performed to confirm their robustness before use. Metabolites, demographic features, clinical characteristics, and uterine Doppler pulsatility index data were evaluated. Area under the receiver operator characteristic curve (AUC), 95% confidence interval (CI), sensitivity, and specificity of the biomarker models were derived. RESULTS Validation testing found that the metabolite-only model had an AUC of 0.835 (95% CI, 0.769-0.941) with a 75% sensitivity and 74.4% specificity and for the metabolites plus uterine Doppler pulsatility index model it was 0.916 (95% CI, 0.836-0.996), 90%, and 88.4%, respectively. Predictive metabolites included arginine and 2-hydroxybutyrate, which are known to be involved in vascular dilation, and insulin resistance and impaired glucose regulation, respectively. CONCLUSION We found confirmatory evidence that first-trimester metabolomic biomarkers can predict future development of early PE.
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Hochrein J, Zacharias HU, Taruttis F, Samol C, Engelmann JC, Spang R, Oefner PJ, Gronwald W. Data Normalization of (1)H NMR Metabolite Fingerprinting Data Sets in the Presence of Unbalanced Metabolite Regulation. J Proteome Res 2015; 14:3217-28. [PMID: 26147738 DOI: 10.1021/acs.jproteome.5b00192] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Data normalization is an essential step in NMR-based metabolomics. Conducted properly, it improves data quality and removes unwanted biases. The choice of the appropriate normalization method is critical and depends on the inherent properties of the data set in question. In particular, the presence of unbalanced metabolic regulation, where the different specimens and cohorts under investigation do not contain approximately equal shares of up- and down-regulated features, may strongly influence data normalization. Here, we demonstrate the suitability of the Shapiro-Wilk test to detect such unbalanced regulation. Next, employing a Latin-square design consisting of eight metabolites spiked into a urine specimen at eight different known concentrations, we show that commonly used normalization and scaling methods fail to retrieve true metabolite concentrations in the presence of increasing amounts of glucose added to simulate unbalanced regulation. However, by learning the normalization parameters on a subset of nonregulated features only, Linear Baseline Normalization, Probabilistic Quotient Normalization, and Variance Stabilization Normalization were found to account well for different dilutions of the samples without distorting the true spike-in levels even in the presence of marked unbalanced metabolic regulation. Finally, the methods described were applied successfully to a real world example of unbalanced regulation, namely, a set of plasma specimens collected from patients with and without acute kidney injury after cardiac surgery with cardiopulmonary bypass use.
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Affiliation(s)
- Jochen Hochrein
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Helena U Zacharias
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Franziska Taruttis
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Claudia Samol
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Julia C Engelmann
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Rainer Spang
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
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Yip LY, Chan ECY. Investigation of Host-Gut Microbiota Modulation of Therapeutic Outcome. Drug Metab Dispos 2015; 43:1619-31. [PMID: 25979259 DOI: 10.1124/dmd.115.063750] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/15/2015] [Indexed: 02/06/2023] Open
Abstract
A broader understanding of factors underlying interindividual variation in pharmacotherapy is important for our pursuit of "personalized medicine." Based on knowledge gleaned from the investigation of human genetics, drug-metabolizing enzymes, and transporters, clinicians and pharmacists are able to tailor pharmacotherapies according to the genotype of patients. However, human host factors only form part of the equation that accounts for heterogeneity in therapeutic outcome. Notably, the gut microbiota possesses wide-ranging metabolic activities that expand the metabolic functions of the human host beyond that encoded by the human genome. In this review, we first illustrate the mechanisms in which gut microbes modulate pharmacokinetics and therapeutic outcome. Second, we discuss the application of metabonomics in deciphering the complex host-gut microbiota interaction in pharmacotherapy. Third, we highlight an integrative approach with particular mention of the investigation of gut microbiota using culture-based and culture-independent techniques to complement the investigation of the host-gut microbiota axes in pharmaceutical research.
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Affiliation(s)
- Lian Yee Yip
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore (L.Y.Y., E.C.Y.C.); and Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore (L.Y.Y.)
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore (L.Y.Y., E.C.Y.C.); and Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore (L.Y.Y.)
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Hariharan R, Hoffman JM, Thomas AS, Soltow QA, Jones DP, Promislow DEL. Invariance and plasticity in the Drosophila melanogaster metabolomic network in response to temperature. BMC SYSTEMS BIOLOGY 2014; 8:139. [PMID: 25540032 PMCID: PMC4302152 DOI: 10.1186/s12918-014-0139-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/11/2014] [Indexed: 12/31/2022]
Abstract
Background Metabolomic responses to extreme thermal stress have recently been investigated in Drosophila melanogaster. However, a network level understanding of metabolomic responses to longer and less drastic temperature changes, which more closely reflect variation in natural ambient temperatures experienced during development and adulthood, is currently lacking. Here we use high-resolution, non-targeted metabolomics to dissect metabolomic changes in D. melanogaster elicited by moderately cool (18°C) or warm (27°C) developmental and adult temperature exposures. Results We find that temperature at which larvae are reared has a dramatic effect on metabolomic network structure measured in adults. Using network analysis, we are able to identify modules that are highly differentially expressed in response to changing developmental temperature, as well as modules whose correlation structure is strongly preserved across temperature. Conclusions Our results suggest that the effect of temperature on the metabolome provides an easily studied and powerful model for understanding the forces that influence invariance and plasticity in biological networks. Electronic supplementary material The online version of this article (doi:10.1186/s12918-014-0139-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ramkumar Hariharan
- Department of Pathology, University of Washington, Box 357705, Seattle, WA, 98195, USA. .,Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Jessica M Hoffman
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| | - Ariel S Thomas
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA. .,Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO, 63108, USA.
| | - Quinlyn A Soltow
- Division of Pulmonary Allergy & Critical Care Medicine, Emory University, Atlanta, GA, 30322, USA. .,Department of Medicine, Clinical Biomarkers Laboratory, Emory University, Atlanta, GA, 30322, USA. .,ClinMet Inc, 3210 Merryfield Row, San Diego, CA, 92121, USA.
| | - Dean P Jones
- Division of Pulmonary Allergy & Critical Care Medicine, Emory University, Atlanta, GA, 30322, USA. .,Department of Medicine, Clinical Biomarkers Laboratory, Emory University, Atlanta, GA, 30322, USA.
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Box 357705, Seattle, WA, 98195, USA. .,Department of Biology, University of Washington, Seattle, WA, 98195, USA.
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Rogers GB, Kozlowska J, Keeble J, Metcalfe K, Fao M, Dowd SE, Mason AJ, McGuckin MA, Bruce KD. Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice. Sci Rep 2014; 4:5437. [PMID: 24961643 PMCID: PMC4069701 DOI: 10.1038/srep05437] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/05/2014] [Indexed: 12/20/2022] Open
Abstract
Despite the fundamental contribution of the gut microbiota to host physiology, the extent of its variation in genetically-identical animals used in research is not known. We report significant divergence in both the composition and metabolism of gut microbiota in genetically-identical adult C57BL/6 mice housed in separate controlled units within a single commercial production facility. The reported divergence in gut microbiota has the potential to confound experimental studies using mammalian models.
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Affiliation(s)
- G. B. Rogers
- Immunity, Infection, and Inflammation Program, Mater Research Institute – University of Queensland, Translational Research Institute, Woolloongabba, Australia
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Bedford Park, Adelaide, Australia
| | - J. Kozlowska
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
| | - J. Keeble
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
| | - K. Metcalfe
- Charles River UK, Manston Rd. Margate, Kent CT9 4LT UK
| | - M. Fao
- Charles River UK, Manston Rd. Margate, Kent CT9 4LT UK
| | - S. E. Dowd
- Molecular Research MR DNA, Shallowater, TX 79363, USA
| | - A. J. Mason
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
| | - M. A. McGuckin
- Immunity, Infection, and Inflammation Program, Mater Research Institute – University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - K. D. Bruce
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
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Hailemariam D, Mandal R, Saleem F, Dunn SM, Wishart DS, Ametaj BN. Identification of predictive biomarkers of disease state in transition dairy cows. J Dairy Sci 2014; 97:2680-93. [PMID: 24630653 DOI: 10.3168/jds.2013-6803] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 01/16/2014] [Indexed: 12/29/2022]
Abstract
In dairy cows, periparturient disease states, such as metritis, mastitis, and laminitis, are leading to increasingly significant economic losses for the dairy industry. Treatments for these pathologies are often expensive, ineffective, or not cost-efficient, leading to production losses, high veterinary bills, or early culling of the cows. Early diagnosis or detection of these conditions before they manifest themselves could lower their incidence, level of morbidity, and the associated economic losses. In an effort to identify predictive biomarkers for postpartum or periparturient disease states in dairy cows, we undertook a cross-sectional and longitudinal metabolomics study to look at plasma metabolite levels of dairy cows during the transition period, before and after becoming ill with postpartum diseases. Specifically we employed a targeted quantitative metabolomics approach that uses direct flow injection mass spectrometry to track the metabolite changes in 120 different plasma metabolites. Blood plasma samples were collected from 12 dairy cows at 4 time points during the transition period (-4 and -1 wk before and 1 and 4 wk after parturition). Out of the 12 cows studied, 6 developed multiple periparturient disorders in the postcalving period, whereas the other 6 remained healthy during the entire experimental period. Multivariate data analysis (principal component analysis and partial least squares discriminant analysis) revealed a clear separation between healthy controls and diseased cows at all 4 time points. This analysis allowed us to identify several metabolites most responsible for separating the 2 groups, especially before parturition and the start of any postpartum disease. Three metabolites, carnitine, propionyl carnitine, and lysophosphatidylcholine acyl C14:0, were significantly elevated in diseased cows as compared with healthy controls as early as 4 wk before parturition, whereas 2 metabolites, phosphatidylcholine acyl-alkyl C42:4 and phosphatidylcholine diacyl C42:6, could be used to discriminate healthy controls from diseased cows 1 wk before parturition. A 3-metabolite plasma biomarker profile was developed that could predict which cows would develop periparturient diseases, up to 4 wk before clinical symptoms appearing, with a sensitivity of 87% and a specificity of 85%. This is the first report showing that periparturient diseases can be predicted in dairy cattle before their development using a multimetabolite biomarker model. Further research is warranted to validate these potential predictive biomarkers.
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Affiliation(s)
- D Hailemariam
- Department of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada T6G 2P5
| | - R Mandal
- Departments of Computer and Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2M9
| | - F Saleem
- Departments of Computer and Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2M9
| | - S M Dunn
- Department of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada T6G 2P5
| | - D S Wishart
- Departments of Computer and Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2M9
| | - B N Ametaj
- Department of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada T6G 2P5.
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Altmäe S, Esteban FJ, Stavreus-Evers A, Simón C, Giudice L, Lessey BA, Horcajadas JA, Macklon NS, D'Hooghe T, Campoy C, Fauser BC, Salamonsen LA, Salumets A. Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. Hum Reprod Update 2014; 20:12-28. [PMID: 24082038 PMCID: PMC3845681 DOI: 10.1093/humupd/dmt048] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 08/04/2013] [Accepted: 08/19/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
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Affiliation(s)
- Signe Altmäe
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | | | - Anneli Stavreus-Evers
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185 Uppsala, Sweden
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad (FIVI) and Instituto Universitario IVI/INCLIVA, Valencia University, 46021 Valencia, Spain
| | - Linda Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143-0132, USA
| | - Bruce A. Lessey
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University Medical Group, Greenville Hospital System, Greenville, South Carolina, SC 29605, USA
| | - Jose A. Horcajadas
- Araid-Hospital Miguel Servet, 50004 Zaragoza, Spain
- Department of Genetics, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Nick S. Macklon
- Department of Obstetrics and Gynaecology, Division of Developmental Origins of Adult Disease, University of Southampton, Princess Anne Hospital, SO16 5YA Southampton, UK
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Thomas D'Hooghe
- Leuven University Fertility Center, Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven (Leuven University), 3000 Leuven, Belgium
| | - Cristina Campoy
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | - Bart C. Fauser
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Lois A. Salamonsen
- Prince Henry's Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Andres Salumets
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- Department of Obstetrics and Gynaecology, University of Tartu, 51014 Tartu, Estonia
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38
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Analyzing methods for path mining with applications in metabolomics. Gene 2013; 534:125-38. [PMID: 24230973 DOI: 10.1016/j.gene.2013.10.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 11/22/2022]
Abstract
Metabolomics is one of the key approaches of systems biology that consists of studying biochemical networks having a set of metabolites, enzymes, reactions and their interactions. As biological networks are very complex in nature, proper techniques and models need to be chosen for their better understanding and interpretation. One of the useful strategies in this regard is using path mining strategies and graph-theoretical approaches that help in building hypothetical models and perform quantitative analysis. Furthermore, they also contribute to analyzing topological parameters in metabolome networks. Path mining techniques can be based on grammars, keys, patterns and indexing. Moreover, they can also be used for modeling metabolome networks, finding structural similarities between metabolites, in-silico metabolic engineering, shortest path estimation and for various graph-based analysis. In this manuscript, we have highlighted some core and applied areas of path-mining for modeling and analysis of metabolic networks.
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39
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Tymoshenko S, Oppenheim RD, Soldati-Favre D, Hatzimanikatis V. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics 2013; 12:316-27. [PMID: 23793264 PMCID: PMC3743259 DOI: 10.1093/bfgp/elt017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project in 2002 provided a comprehensive foundation for functional genomic studies on this pathogen in the following decade. Over this period, a large spectrum of experimental approaches has been deployed to improve and expand the scope of functionally annotated genes. Meanwhile, rapidly evolving methods of systems biology have also begun to contribute to a more global understanding of various aspects of the biology and pathogenesis of malaria. Herein we provide an overview on metabolic modelling, which has the capability to integrate information from functional genomics studies in P. falciparum and guide future malaria research efforts towards the identification of novel candidate drug targets.
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Affiliation(s)
- Stepan Tymoshenko
- Institute of Chemical Engineering, Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, CH-1015, Switzerland.
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40
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Garcia-Manteiga JM. Data Analysis and Interpretation in Metabolomics. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Metabolomics represents the new ‘omics’ approach of the functional genomics era. It consists in the identification and quantification of all small molecules, namely metabolites, in a given biological system. While metabolomics refers to the analysis of any possible biological system, metabonomics is specifically applied to disease and physiopathological situations. The data collected within these approaches is highly integrative of the other higher levels and is hence amenable to be explored with a top-down systems biology point of view. The aim of this chapter is to give a global view of the state of the art in metabolomics describing the two analytical techniques usually used to give rise to this kind of data, nuclear magnetic resonance, NMR, and mass spectrometry. In addition, the author will focus on the different data analysis tools that can be applied to such studies to extract information with special interest at the attempts to integrate metabolomics with other ‘omics’ approaches and its relevance in systems biology modeling.
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Bohra R, Klepacki J, Klawitter J, Klawitter J, Thurman J, Christians U. Proteomics and metabolomics in renal transplantation-quo vadis? Transpl Int 2013; 26:225-41. [PMID: 23350848 PMCID: PMC4006577 DOI: 10.1111/tri.12003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 05/07/2012] [Accepted: 10/07/2012] [Indexed: 12/13/2022]
Abstract
The improvement of long-term transplant organ and patient survival remains a critical challenge following kidney transplantation. Proteomics and biochemical profiling (metabolomics) may allow for the detection of early changes in cell signal transduction regulation and biochemistry with high sensitivity and specificity. Hence, these analytical strategies hold the promise to detect and monitor disease processes and drug effects before histopathological and pathophysiological changes occur. In addition, they will identify enriched populations and enable individualized drug therapy. However, proteomics and metabolomics have not yet lived up to such high expectations. Renal transplant patients are highly complex, making it difficult to establish cause-effect relationships between surrogate markers and disease processes. Appropriate study design, adequate sample handling, storage and processing, quality and reproducibility of bioanalytical multi-analyte assays, data analysis and interpretation, mechanistic verification, and clinical qualification (=establishment of sensitivity and specificity in adequately powered prospective clinical trials) are important factors for the success of molecular marker discovery and development in renal transplantation. However, a newly developed and appropriately qualified molecular marker can only be successful if it is realistic that it can be implemented in a clinical setting. The development of combinatorial markers with supporting software tools is an attractive goal.
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Affiliation(s)
- Rahul Bohra
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
| | - Jacek Klepacki
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
| | - Jelena Klawitter
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
- Renal Medicine, University of Colorado Denver, Aurora, USA
| | - Jost Klawitter
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
| | - Joshua Thurman
- Renal Medicine, University of Colorado Denver, Aurora, USA
| | - Uwe Christians
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
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42
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Booth SC, Weljie AM, Turner RJ. Computational tools for the secondary analysis of metabolomics experiments. Comput Struct Biotechnol J 2013; 4:e201301003. [PMID: 24688685 PMCID: PMC3962093 DOI: 10.5936/csbj.201301003] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 12/17/2012] [Accepted: 12/24/2012] [Indexed: 01/30/2023] Open
Abstract
Metabolomics experiments have become commonplace in a wide variety of disciplines. By identifying and quantifying metabolites researchers can achieve a systems level understanding of metabolism. These studies produce vast swaths of data which are often only lightly interpreted due to the overwhelmingly large amount of variables that are measured. Recently, a number of computational tools have been developed which enable much deeper analysis of metabolomics data. These data have been difficult to interpret as understanding the connections between dozens of altered metabolites has often relied on the biochemical knowledge of researchers and their speculations. Modern biochemical databases provide information about the interconnectivity of metabolism which can be automatically polled using metabolomics secondary analysis tools. Starting with lists of altered metabolites, there are two main types of analysis: enrichment analysis computes which metabolic pathways have been significantly altered whereas metabolite mapping contextualizes the abundances and significances of measured metabolites into network visualizations. Many different tools have been developed for one or both of these applications. In this review the functionality and use of these software is discussed. Together these novel secondary analysis tools will enable metabolomics researchers to plumb the depths of their data and produce farther reaching biological conclusions than ever before.
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Affiliation(s)
- Sean C Booth
- Department of Biological Sciences, University of Calgary, Calgary, AB. 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Aalim M Weljie
- Department of Pharmacology, University of Pennsylvania, Philadelphia, United States
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, AB. 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
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43
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Spégel P, Ekholm E, Tuomi T, Groop L, Mulder H, Filipsson K. Metabolite profiling reveals normal metabolic control in carriers of mutations in the glucokinase gene (MODY2). Diabetes 2013; 62:653-61. [PMID: 23139355 PMCID: PMC3554352 DOI: 10.2337/db12-0827] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mutations in the gene encoding glucokinase (GCK) cause a mild hereditary form of diabetes termed maturity-onset diabetes of the young (MODY)2 or GCK-MODY. The disease does not progress over time, and diabetes complications rarely develop. It has therefore been suggested that GCK-MODY represents a metabolically compensated condition, but experimental support for this notion is lacking. Here, we profiled metabolites in serum from patients with MODY1 (HNF4A), MODY2 (GCK), MODY3 (HNF1A), and type 2 diabetes and from healthy individuals to characterize metabolic perturbations caused by specific mutations. Analysis of four GCK-MODY patients revealed a metabolite pattern similar to that of healthy individuals, while other forms of diabetes differed markedly in their metabolite profiles. Furthermore, despite elevated glucose concentrations, carriers of GCK mutations showed lower levels of free fatty acids and triglycerides than healthy control subjects. The metabolite profiling was confirmed by enzymatic assays and replicated in a cohort of 11 GCK-MODY patients. Elevated levels of fatty acids are known to associate with β-cell dysfunction, insulin resistance, and increased incidence of late complications. Our results show that GCK-MODY represents a metabolically normal condition, which may contribute to the lack of late complications and the nonprogressive nature of the disease.
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Affiliation(s)
- Peter Spégel
- Unit of Molecular Metabolism, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Malmö, Sweden.
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44
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Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K. First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol 2013; 208:58.e1-7. [PMID: 23159745 DOI: 10.1016/j.ajog.2012.11.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 11/04/2012] [Accepted: 11/08/2012] [Indexed: 12/17/2022]
Abstract
OBJECTIVE We sought to identify first-trimester maternal serum biomarkers for the prediction of late-onset preeclampsia (PE) using metabolomic analysis. STUDY DESIGN In a case-control study, nuclear magnetic resonance-based metabolomic analysis was performed on first-trimester maternal serum between 11(+0)-13(+6) weeks of gestation. There were 30 cases of late-onset PE, i.e., requiring delivery ≥37 weeks, and 59 unaffected controls. The concentrations of 40 metabolites were compared between the 2 groups. We also compared 30 early-onset cases to the late-onset group. RESULTS A total of 14 metabolites were significantly elevated and 3 significantly reduced in first-trimester serum of late-onset PE patients. A complex model consisting of multiple metabolites and maternal demographic characteristics had a 76.6% sensitivity at 100% specificity for PE detection. A simplified model using fewer predictors yielded 60% sensitivity at 96.6% specificity. Strong separation of late- vs early-onset PE groups was achieved. CONCLUSION Significant differences in the first-trimester metabolites were noted in women who went on to developed late-onset PE and between early- and late-onset PE.
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45
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Clinical metabolomics: the next stage of clinical biochemistry. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2012; 10 Suppl 2:s19-24. [PMID: 22890264 DOI: 10.2450/2012.005s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hochrein J, Klein MS, Zacharias HU, Li J, Wijffels G, Schirra HJ, Spang R, Oefner PJ, Gronwald W. Performance Evaluation of Algorithms for the Classification of Metabolic 1H NMR Fingerprints. J Proteome Res 2012; 11:6242-51. [DOI: 10.1021/pr3009034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jochen Hochrein
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Matthias S. Klein
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Helena U. Zacharias
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Juan Li
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, QLD
4067, Australia
| | - Gene Wijffels
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, QLD
4067, Australia
| | - Horst Joachim Schirra
- Centre for
Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rainer Spang
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Peter J. Oefner
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
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47
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Chagoyen M, Pazos F. Tools for the functional interpretation of metabolomic experiments. Brief Bioinform 2012; 14:737-44. [DOI: 10.1093/bib/bbs055] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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48
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Kohl SM, Klein MS, Hochrein J, Oefner PJ, Spang R, Gronwald W. State-of-the art data normalization methods improve NMR-based metabolomic analysis. Metabolomics 2012; 8:146-160. [PMID: 22593726 PMCID: PMC3337420 DOI: 10.1007/s11306-011-0350-z] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 08/01/2011] [Indexed: 12/20/2022]
Abstract
Extracting biomedical information from large metabolomic datasets by multivariate data analysis is of considerable complexity. Common challenges include among others screening for differentially produced metabolites, estimation of fold changes, and sample classification. Prior to these analysis steps, it is important to minimize contributions from unwanted biases and experimental variance. This is the goal of data preprocessing. In this work, different data normalization methods were compared systematically employing two different datasets generated by means of nuclear magnetic resonance (NMR) spectroscopy. To this end, two different types of normalization methods were used, one aiming to remove unwanted sample-to-sample variation while the other adjusts the variance of the different metabolites by variable scaling and variance stabilization methods. The impact of all methods tested on sample classification was evaluated on urinary NMR fingerprints obtained from healthy volunteers and patients suffering from autosomal polycystic kidney disease (ADPKD). Performance in terms of screening for differentially produced metabolites was investigated on a dataset following a Latin-square design, where varied amounts of 8 different metabolites were spiked into a human urine matrix while keeping the total spike-in amount constant. In addition, specific tests were conducted to systematically investigate the influence of the different preprocessing methods on the structure of the analyzed data. In conclusion, preprocessing methods originally developed for DNA microarray analysis, in particular, Quantile and Cubic-Spline Normalization, performed best in reducing bias, accurately detecting fold changes, and classifying samples. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-011-0350-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefanie M. Kohl
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Matthias S. Klein
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Jochen Hochrein
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Peter J. Oefner
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Rainer Spang
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
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49
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Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K. Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med 2012; 25:1840-7. [PMID: 22494326 DOI: 10.3109/14767058.2012.680254] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVE To evaluate the use of metabolomics for the first-trimester detection of maternal metabolic dysfunction and prediction of subsequent development of early-onset preeclampsia (PE). STUDY DESIGN This was a case-control study of maternal plasma samples collected at 11-13 weeks' gestation from 30 women who had subsequently developed PE requiring delivery before 34 weeks and 60 unaffected controls. Nuclear magnetic Resonance (NMR) spectroscopy was used to identify and quantify metabolomic changes in cases versus controls. Both genetic computing and standard statistical analyses were performed to predict the development of PE from the metabolite concentrations alone as well as the combination of metabolite concentrations with maternal characteristics and first-trimester uterine artery Doppler pulsatility index (PI). RESULTS Significant differences between cases and controls were found for 20 metabolites. A combination of four of these metabolites (citrate, glycerol, hydroxyisovalerate, and methionine) appeared highly predictive of PE with an estimated detection rate of 75.9%, at a false-positive rate (FPR) of 4.9%. The predictive performance was improved by the addition of uterine artery Doppler PI and fetal crown-rump length (CRL) and with an estimated detection rate of 82.6%, at a FPR of 1.6%. CONCLUSION A profound change in the first-trimester metabolite profile was noted in women who had subsequently developed early-onset PE. Preliminary algorithms appeared highly sensitive for first trimester prediction of early onset PE.
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Affiliation(s)
- Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48226, USA.
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50
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Silva AM, Cordeiro-da-Silva A, Coombs GH. Metabolic variation during development in culture of Leishmania donovani promastigotes. PLoS Negl Trop Dis 2011; 5:e1451. [PMID: 22206037 PMCID: PMC3243725 DOI: 10.1371/journal.pntd.0001451] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/10/2011] [Indexed: 11/28/2022] Open
Abstract
The genome sequencing of several Leishmania species has provided immense amounts of data and allowed the prediction of the metabolic pathways potentially operating. Subsequent genetic and proteomic studies have identified stage-specific proteins and putative virulence factors but many aspects of the metabolic adaptations of Leishmania remain to be elucidated. In this study, we have used an untargeted metabolomics approach to analyze changes in the metabolite profile as promastigotes of L. donovani develop during in vitro cultures from logarithmic to stationary phase. The results show that the metabolomes of promastigotes on days 3–6 of culture differ significantly from each other, consistent with there being distinct developmental changes. Most notable were the structural changes in glycerophospholipids and increase in the abundance of sphingolipids and glycerolipids as cells progress from logarithmic to stationary phase. Leishmania infections are considered neglected tropical diseases as the parasites affect millions of people worldwide but there are limited research efforts aimed at obtaining vaccines and new drugs. Leishmania has a digenetic life cycle alternating between promastigote forms, which develop in the sand-fly, the vector of the disease, and an amastigote form, which grows in mammals after being bitten by an infected sand-fly. In vitro studies with the promastigote forms are routinely used to gain insights about the parasite's cell biology. Little is known about how the different promastigotes forms are metabolically adapted to their particular micro-environment in the host or how they are pre-adapted metabolically for infecting a mammal, thus we have undertaken a study of the metabolite profile of L. donovani promastigotes in order to gain an understanding of the changes that occur during promastigote development. The analysis has revealed that the changes in promastigotes' metabolome between days 3 and 6 take place in a progressive manner; however major differences were observed when comparing the promastigotes on days 3 and 6. An increase in lipid abundance as promastigote development occurred was notable and is likely to reflect remodelling of the parasite's surface in readiness for infecting a mammal.
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Affiliation(s)
- Ana Marta Silva
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Laboratório de Ciências Biológicas, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal
| | - Anabela Cordeiro-da-Silva
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Laboratório de Ciências Biológicas, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal
| | - Graham H. Coombs
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail:
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