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Thomas DM, Knight R, Gilbert JA, Cornelis MC, Gantz MG, Burdekin K, Cummiskey K, Sumner SCJ, Pathmasiri W, Sazonov E, Gabriel KP, Dooley EE, Green MA, Pfluger A, Kleinberg S. Transforming Big Data into AI-ready data for nutrition and obesity research. Obesity (Silver Spring) 2024; 32:857-870. [PMID: 38426232 PMCID: PMC11180473 DOI: 10.1002/oby.23989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 03/02/2024]
Abstract
OBJECTIVE Big Data are increasingly used in obesity and nutrition research to gain new insights and derive personalized guidance; however, this data in raw form are often not usable. Substantial preprocessing, which requires machine learning (ML), human judgment, and specialized software, is required to transform Big Data into artificial intelligence (AI)- and ML-ready data. These preprocessing steps are the most complex part of the entire modeling pipeline. Understanding the complexity of these steps by the end user is critical for reducing misunderstanding, faulty interpretation, and erroneous downstream conclusions. METHODS We reviewed three popular obesity/nutrition Big Data sources: microbiome, metabolomics, and accelerometry. The preprocessing pipelines, specialized software, challenges, and how decisions impact final AI- and ML-ready products were detailed. RESULTS Opportunities for advances to improve quality control, speed of preprocessing, and intelligent end user consumption were presented. CONCLUSIONS Big Data have the exciting potential for identifying new modifiable factors that impact obesity research. However, to ensure accurate interpretation of conclusions arising from Big Data, the choices involved in preparing AI- and ML-ready data need to be transparent to investigators and clinicians relying on the conclusions.
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Affiliation(s)
- Diana M. Thomas
- Department of Mathematical Sciences, United States Military Academy, West Point, NY 10996
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of San Diego, La Jolla, CA 92037
| | - Jack A. Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037
| | - Marilyn C. Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Marie G. Gantz
- RTI International, Biostatics and Epidemiology Division, Research Triangle Park, NC 27709
| | - Kate Burdekin
- RTI International, Biostatics and Epidemiology Division, Research Triangle Park, NC 27709
| | - Kevin Cummiskey
- Department of Mathematical Sciences, United States Military Academy, West Point, NY 10996
| | - Susan C. J. Sumner
- Department of Nutrition, Nutrition Research Institute, UNC Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081
| | - Wimal Pathmasiri
- Department of Nutrition, Nutrition Research Institute, UNC Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081
| | - Edward Sazonov
- Electrical and Computer Engineering Department, The University of Alabama, Tuscaloosa, AL 35487
| | - Kelley Pettee Gabriel
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL 35294
| | - Erin E. Dooley
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL 35294
| | - Mark A. Green
- Department of Geography & Planning, University of Liverpool, Liverpool, L69 3BX, UK
| | - Andrew Pfluger
- Department of Geography and Environmental Engineering, United States Military Academy, West Point, NY 10996
| | - Samantha Kleinberg
- Computer Science Department, Stevens Institute of Technology, Hoboken, NJ 07030
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Favari C, Rinaldi de Alvarenga JF, Sánchez-Martínez L, Tosi N, Mignogna C, Cremonini E, Manach C, Bresciani L, Del Rio D, Mena P. Factors driving the inter-individual variability in the metabolism and bioavailability of (poly)phenolic metabolites: A systematic review of human studies. Redox Biol 2024; 71:103095. [PMID: 38428187 PMCID: PMC10912651 DOI: 10.1016/j.redox.2024.103095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
This systematic review provides an overview of the available evidence on the inter-individual variability (IIV) in the absorption, distribution, metabolism, and excretion (ADME) of phenolic metabolites and its determinants. Human studies were included investigating the metabolism and bioavailability of (poly)phenols and reporting IIV. One hundred fifty-three studies met the inclusion criteria. Inter-individual differences were mainly related to gut microbiota composition and activity but also to genetic polymorphisms, age, sex, ethnicity, BMI, (patho)physiological status, and physical activity, depending on the (poly)phenol sub-class considered. Most of the IIV has been poorly characterised. Two major types of IIV were observed. One resulted in metabolite gradients that can be further classified into high and low excretors, as seen for all flavonoids, phenolic acids, prenylflavonoids, alkylresorcinols, and hydroxytyrosol. The other type of IIV is based on clusters of individuals defined by qualitative differences (producers vs. non-producers), as for ellagitannins (urolithins), isoflavones (equol and O-DMA), resveratrol (lunularin), and preliminarily for avenanthramides (dihydro-avenanthramides), or by quali-quantitative metabotypes characterized by different proportions of specific metabolites, as for flavan-3-ols, flavanones, and even isoflavones. Future works are needed to shed light on current open issues limiting our understanding of this phenomenon that likely conditions the health effects of dietary (poly)phenols.
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Affiliation(s)
- Claudia Favari
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy.
| | | | - Lorena Sánchez-Martínez
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy; Department of Food Technology, Food Science and Nutrition, Faculty of Veterinary Sciences, Regional Campus of International Excellence 'Campus Mare Nostrum', Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University Clinical Hospital 'Virgen de La Arrixaca', Universidad de Murcia, Espinardo, Murcia, Spain
| | - Nicole Tosi
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy
| | - Cristiana Mignogna
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy
| | - Eleonora Cremonini
- Department of Nutrition, University of California, Davis, CA, USA; Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Claudine Manach
- Université Clermont Auvergne, INRAE, Human Nutrition Unit, Clermont-Ferrand, France
| | - Letizia Bresciani
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy
| | - Daniele Del Rio
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, 43124, Parma, Italy
| | - Pedro Mena
- Human Nutrition Unit, Department of Food and Drugs, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, 43124, Parma, Italy
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Fu J, Zhu F, Xu CJ, Li Y. Metabolomics meets systems immunology. EMBO Rep 2023; 24:e55747. [PMID: 36916532 PMCID: PMC10074123 DOI: 10.15252/embr.202255747] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/24/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.
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Affiliation(s)
- Jianbo Fu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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Zhang R, Meng J, Wang X, Pu L, Zhao T, Huang Y, Han L. Metabolomics of ischemic stroke: insights into risk prediction and mechanisms. Metab Brain Dis 2022; 37:2163-2180. [PMID: 35612695 DOI: 10.1007/s11011-022-01011-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
Abstract
Ischemic stroke (IS) is the most prevalent type of stroke. The early diagnosis and prognosis of IS are crucial for successful therapy and early intervention. Metabolomics, a tool in systems biology based on several innovative technologies, can be used to identify disease biomarkers and unveil underlying pathophysiological processes. Accordingly, in recent years, an increasing number of studies have identified metabolites from cerebral ischemia patients and animal models that could improve the diagnosis of IS and prediction of its outcome. In this paper, metabolomic research is comprehensively reviewed with a focus on describing the metabolic changes and related pathways associated with IS. Most clinical studies use biofluids (e.g., blood or plasma) because their collection is minimally invasive and they are ideal for analyzing changes in metabolites in patients of IS. We review the application of animal models in metabolomic analyses aimed at investigating potential mechanisms of IS and developing novel therapeutic approaches. In addition, this review presents the strengths and limitations of current metabolomic studies on IS, providing a reference for future related studies.
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Affiliation(s)
- Ruijie Zhang
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
| | - Jiajia Meng
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Xihu District Center for Disease Control and Prevention, Hangzhou, 310013, Zhejiang, China
| | - Xiaojie Wang
- Department of Neurology, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, 518067, Guangdong, China
| | - Liyuan Pu
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
| | - Tian Zhao
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
| | - Yi Huang
- Department of Neurosurgery, Ningbo First Hospital, Ningbo, 315010, Zhejiang, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, 315010, Zhejiang, China.
- Medical Research Center, Ningbo First Hospital, Ningbo, 315010, Zhejiang, China.
| | - Liyuan Han
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China.
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5
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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6
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Mehanna M, McDonough CW, Smith SM, Gong Y, Gums JG, Chapman AB, Johnson JA, Cooper-DeHoff RM. Influence of Genetic West African Ancestry on Metabolomics among Hypertensive Patients. Metabolites 2022; 12:metabo12090783. [PMID: 36144188 PMCID: PMC9506508 DOI: 10.3390/metabo12090783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 12/02/2022] Open
Abstract
Patients with higher genetic West African ancestry (GWAA) have hypertension (HTN) that is more difficult to treat and have higher rates of cardiovascular diseases (CVD) and differential responses to antihypertensive drugs than those with lower GWAA. The mechanisms underlying these disparities are poorly understood. Using data from 84 ancestry-informative markers in US participants from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) and PEAR-2 trials, the GWAA proportion was estimated. Using multivariable linear regression, the baseline levels of 886 metabolites were compared between PEAR participants with GWAA < 45% and those with GWAA ≥ 45% to identify differential metabolites and metabolic clusters. Metabolites with a false discovery rate (FDR) < 0.2 were used to create metabolic clusters, and a cluster analysis was conducted. Differential clusters were then tested for replication in PEAR-2 participants. We identified 353 differential metabolites (FDR < 0.2) between PEAR participants with GWAA < 45% (n = 383) and those with GWAA ≥ 45% (n = 250), which were used to create 24 metabolic clusters. Of those, 13 were significantly different between groups (Bonferroni p < 0.002). Four clusters, plasmalogen and lysoplasmalogen, sphingolipid metabolism and ceramide, cofactors and vitamins, and the urea cycle, were replicated in PEAR-2 (Bonferroni p < 0.0038) and have been previously linked to HTN and CVD. Our findings may give insights into the mechanisms underlying HTN racial disparities.
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Affiliation(s)
- Mai Mehanna
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Caitrin W. McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Steven M. Smith
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Department of Pharmaceutical Outcomes & Policy, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - John G. Gums
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Arlene B. Chapman
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Rhonda M. Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Correspondence: ; Tel.: +1-(352)-273-6184
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7
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Narduzzi L, Agulló V, Favari C, Tosi N, Mignogna C, Crozier A, Rio DD, Mena P. (Poly)phenolic compounds and gut microbiome: new opportunities for personalized nutrition. MICROBIOME RESEARCH REPORTS 2022; 1:16. [PMID: 38046361 PMCID: PMC10688808 DOI: 10.20517/mrr.2022.06] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/05/2023]
Abstract
For decades, (poly)phenols have been linked to cardiometabolic health, but population heterogeneity limits their apparent efficacy and the development of tailored, practical protocols in dietary interventions. This heterogeneity is likely determined by the existence of different metabotypes, sub-populations of individuals metabolizing some classes of (poly)phenols differently. The gut microbiota plays a major role in this process. The impact of microbiota-related phenolic metabotypes on cardiometabolic health is becoming evident, although the picture is still incomplete, and data are absent for some classes of (poly)phenols. The lack of a complete understanding of the main microbial actors involved in the process complicates the picture. Elucidation of the mechanisms behind phenolic metabotypes requires novel experimental designs that can dissect the inter-individual variability. This paper, in addition to providing an overview on the current state-of-the-art, proposes wider metabotyping approaches as a means of paving the way towards effective personalized nutrition with dietary (poly)phenols.
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Affiliation(s)
- Luca Narduzzi
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
| | - Vicente Agulló
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
- Phytochemistry and Healthy Foods Lab (LabFAS), Food Science and Technology Department (CEBAS-CSIC), University Campus of Espinardo, Murcia 30100, Spain
| | - Claudia Favari
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
| | - Nicole Tosi
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
| | - Cristiana Mignogna
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
| | - Alan Crozier
- Department of Chemistry, King Saud University, Riyadh 11451, Saudi Arabia
- School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Daniele Del Rio
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11/A, Parma 43124, Italy
| | - Pedro Mena
- Human Nutrition Unit, Department of Food & Drug, University of Parma, Parma 43125, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11/A, Parma 43124, Italy
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8
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Price EJ, Vitale CM, Miller GW, David A, Barouki R, Audouze K, Walker DI, Antignac JP, Coumoul X, Bessonneau V, Klánová J. Merging the exposome into an integrated framework for “omics” sciences. iScience 2022; 25:103976. [PMID: 35310334 PMCID: PMC8924626 DOI: 10.1016/j.isci.2022.103976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The exposome concept encourages holistic consideration of the non-genetic factors (environmental exposures including lifestyle) that influence an individual’s health over their life course. However, disconnect between the concept and practical application has promoted divergent interpretations of the exposome across disciplines and reinforced separation of the environmental (emphasizing exposures) and biological (emphasizing responses) research communities. In particular, while knowledge of biological responses can help to distinguish actual (i.e. experienced) from potential exposures, the inclusion of endogenous processes has generated confusion about the position of the exposome in a multi-omics systems biology context. We propose a reattribution of “exposome” to exclusively represent the totality of contact with external factors that a biological entity experiences, and introduce the term “functional exposomics” to denote the systematic study of exposure-phenotype interaction. This reoriented definition of the exposome allows a more readily integrable dataset for multi-omics and systems biology research. Reattribution of exposome concept to exclusively represent environmental exposures Generalized the exposome concept for all levels of biological organization Functional exposome presented as the totality of exposure-phenotype interaction
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9
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Jones B, Sands C, Alexiadou K, Minnion J, Tharakan G, Behary P, Ahmed AR, Purkayastha S, Lewis MR, Bloom S, Li JV, Tan TM. The Metabolomic Effects of Tripeptide Gut Hormone Infusion Compared to Roux-en-Y Gastric Bypass and Caloric Restriction. J Clin Endocrinol Metab 2022; 107:e767-e782. [PMID: 34460933 PMCID: PMC8764224 DOI: 10.1210/clinem/dgab608] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Indexed: 12/23/2022]
Abstract
CONTEXT The gut-derived peptide hormones glucagon-like peptide-1 (GLP-1), oxyntomodulin (OXM), and peptide YY (PYY) are regulators of energy intake and glucose homeostasis and are thought to contribute to the glucose-lowering effects of bariatric surgery. OBJECTIVE To establish the metabolomic effects of a combined infusion of GLP-1, OXM, and PYY (tripeptide GOP) in comparison to a placebo infusion, Roux-en-Y gastric bypass (RYGB) surgery, and a very low-calorie diet (VLCD). DESIGN AND SETTING Subanalysis of a single-blind, randomized, placebo-controlled study of GOP infusion (ClinicalTrials.gov NCT01945840), including VLCD and RYGB comparator groups. PATIENTS AND INTERVENTIONS Twenty-five obese patients with type 2 diabetes or prediabetes were randomly allocated to receive a 4-week subcutaneous infusion of GOP (n = 14) or 0.9% saline control (n = 11). An additional 22 patients followed a VLCD, and 21 underwent RYGB surgery. MAIN OUTCOME MEASURES Plasma and urine samples collected at baseline and 4 weeks into each intervention were subjected to cross-platform metabolomic analysis, followed by unsupervised and supervised modeling approaches to identify similarities and differences between the effects of each intervention. RESULTS Aside from glucose, very few metabolites were affected by GOP, contrasting with major metabolomic changes seen with VLCD and RYGB. CONCLUSIONS Treatment with GOP provides a powerful glucose-lowering effect but does not replicate the broader metabolomic changes seen with VLCD and RYGB. The contribution of these metabolomic changes to the clinical benefits of RYGB remains to be elucidated.
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MESH Headings
- Adult
- Aged
- Blood Glucose/analysis
- Caloric Restriction/methods
- Caloric Restriction/statistics & numerical data
- Diabetes Mellitus, Type 2/blood
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/therapy
- Diabetes Mellitus, Type 2/urine
- Drug Therapy, Combination/methods
- Female
- Gastric Bypass/methods
- Gastric Bypass/statistics & numerical data
- Gastrointestinal Hormones/administration & dosage
- Glucagon-Like Peptide 1/administration & dosage
- Humans
- Infusions, Subcutaneous
- Male
- Metabolomics/statistics & numerical data
- Middle Aged
- Obesity, Morbid/blood
- Obesity, Morbid/metabolism
- Obesity, Morbid/therapy
- Obesity, Morbid/urine
- Oxyntomodulin/administration & dosage
- Peptide YY/administration & dosage
- Single-Blind Method
- Treatment Outcome
- Weight Loss
- Young Adult
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Affiliation(s)
- Ben Jones
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Caroline Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Kleopatra Alexiadou
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - James Minnion
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - George Tharakan
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Preeshila Behary
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Ahmed R Ahmed
- Department of Surgery and Cancer, Imperial College Healthcare NHS Trust, London, UK
| | - Sanjay Purkayastha
- Department of Surgery and Cancer, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew R Lewis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Stephen Bloom
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jia V Li
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Tricia M Tan
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Correspondence: Tricia M. Tan, MB, ChB, BSc, PhD, FRCP, FRCPath, 6th Floor, Commonwealth Building, Hammersmith Campus, Imperial College London, London W12 0HS, UK.
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10
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Varshavi D, Varshavi D, McCarthy N, Veselkov K, Keun HC, Everett JR. Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines. Metabolomics 2021; 17:104. [PMID: 34822010 PMCID: PMC8616861 DOI: 10.1007/s11306-021-01852-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/31/2021] [Indexed: 12/02/2022]
Abstract
INTRODUCTION KRAS was one of the earliest human oncogenes to be described and is one of the most commonly mutated genes in different human cancers, including colorectal cancer. Despite KRAS mutants being known driver mutations, KRAS has proved difficult to target therapeutically, necessitating a comprehensive understanding of the molecular mechanisms underlying KRAS-driven cellular transformation. OBJECTIVES To investigate the metabolic signatures associated with single copy mutant KRAS in isogenic human colorectal cancer cells and to determine what metabolic pathways are affected. METHODS Using NMR-based metabonomics, we compared wildtype (WT)-KRAS and mutant KRAS effects on cancer cell metabolism using metabolic profiling of the parental KRAS G13D/+ HCT116 cell line and its isogenic, derivative cell lines KRAS +/- and KRAS G13D/-. RESULTS Mutation in the KRAS oncogene leads to a general metabolic remodelling to sustain growth and counter stress, including alterations in the metabolism of amino acids and enhanced glutathione biosynthesis. Additionally, we show that KRASG13D/+ and KRASG13D/- cells have a distinct metabolic profile characterized by dysregulation of TCA cycle, up-regulation of glycolysis and glutathione metabolism pathway as well as increased glutamine uptake and acetate utilization. CONCLUSIONS Our study showed the effect of a single point mutation in one KRAS allele and KRAS allele loss in an isogenic genetic background, hence avoiding confounding genetic factors. Metabolic differences among different KRAS mutations might play a role in their different responses to anticancer treatments and hence could be exploited as novel metabolic vulnerabilities to develop more effective therapies against oncogenic KRAS.
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Affiliation(s)
- Dorna Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Nicola McCarthy
- Horizon Discovery Ltd., Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 ONN, UK
| | - Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK.
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11
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Metabolomics Signature of Plasma Renin Activity and Linkage with Blood Pressure Response to Beta Blockers and Thiazide Diuretics in Hypertensive European American Patients. Metabolites 2021; 11:metabo11090645. [PMID: 34564461 PMCID: PMC8466669 DOI: 10.3390/metabo11090645] [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: 08/21/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/13/2023] Open
Abstract
Plasma renin activity (PRA) is a predictive biomarker of blood pressure (BP) response to antihypertensives in European–American hypertensive patients. We aimed to identify the metabolic signatures of baseline PRA and the linkages with BP response to β-blockers and thiazides. Using data from the Pharmacogenomic Evaluation of Antihypertensive Responses-2 (PEAR-2) trial, multivariable linear regression adjusting for age, sex and baseline systolic-BP (SBP) was performed on European–American individuals treated with metoprolol (n = 198) and chlorthalidone (n = 181), to test associations between 856 metabolites and baseline PRA. Metabolites with a false discovery rate (FDR) < 0.05 or p < 0.01 were tested for replication in 463 European–American individuals treated with atenolol or hydrochlorothiazide. Replicated metabolites were then tested for validation based on the directionality of association with BP response. Sixty-three metabolites were associated with baseline PRA, of which nine, including six lipids, were replicated. Of those replicated, two metabolites associated with higher baseline PRA were validated: caprate was associated with greater metoprolol SBP response (β = −1.7 ± 0.6, p = 0.006) and sphingosine-1-phosphate was associated with reduced hydrochlorothiazide SBP response (β = 7.6 ± 2.8, p = 0.007). These metabolites are clustered with metabolites involved in sphingolipid, phospholipid, and purine metabolic pathways. The identified metabolic signatures provide insights into the mechanisms underlying BP response.
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12
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Horvath TD, Dagan S, Scaraffia PY. Unraveling mosquito metabolism with mass spectrometry-based metabolomics. Trends Parasitol 2021; 37:747-761. [PMID: 33896683 PMCID: PMC8282712 DOI: 10.1016/j.pt.2021.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Nearly half a million people die annually due to mosquito-borne diseases. Despite aggressive mosquito population-control efforts, current strategies are limited in their ability to control these vectors. A better understanding of mosquito metabolism through modern approaches can contribute to the discovery of novel metabolic targets and/or regulators and lead to the development of better mosquito-control strategies. Currently, cutting-edge technologies such as gas or liquid chromatography-mass spectrometry-based metabolomics are considered 'mature technologies' in many life-science disciplines but are still an emerging area of research in medical entomology. This review primarily discusses recent developments and progress in the application of mass spectrometry-based metabolomics to answer multiple biological questions related to mosquito metabolism.
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Affiliation(s)
- Thomas D Horvath
- Department of Immunology and Pathology, Baylor College of Medicine, and Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Shai Dagan
- Israel Institute for Biological Research, Ness Ziona, Israel, 74100, Israel
| | - Patricia Y Scaraffia
- Department of Tropical Medicine and Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
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13
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Fu J, Zhang Y, Liu J, Lian X, Tang J, Zhu F. Pharmacometabonomics: data processing and statistical analysis. Brief Bioinform 2021; 22:6236068. [PMID: 33866355 DOI: 10.1093/bib/bbab138] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Individual variations in drug efficacy, side effects and adverse drug reactions are still challenging that cannot be ignored in drug research and development. The aim of pharmacometabonomics is to better understand the pharmacokinetic properties of drugs and monitor the drug effects on specific metabolic pathways. Here, we systematically reviewed the recent technological advances in pharmacometabonomics for better understanding the pathophysiological mechanisms of diseases as well as the metabolic effects of drugs on bodies. First, the advantages and disadvantages of all mainstream analytical techniques were compared. Second, many data processing strategies including filtering, missing value imputation, quality control-based correction, transformation, normalization together with the methods implemented in each step were discussed. Third, various feature selection and feature extraction algorithms commonly applied in pharmacometabonomics were described. Finally, the databases that facilitate current pharmacometabonomics were collected and discussed. All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jin Liu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Xichen Lian
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jing Tang
- Department of Bioinformatics in Chongqing Medical University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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14
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Metabolomics Analysis of Viral Therapeutics. Methods Mol Biol 2021. [PMID: 33108663 DOI: 10.1007/978-1-0716-1012-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Virotherapy, enabled by recent advances in the transdisciplinary field of biotechnology, has emerged as a powerful tool for use in anticancer treatment, gene therapy, immunotherapy, etc. Examining the effects of viruses and virus-derived immune-modulating therapeutics is of great fundamental and clinical interest. Here we describe a sample preparation protocol for metabolite extraction from virus-infected tissue, in addition to liquid chromatography-mass spectrometry conditions essential for subsequent analysis. This metabolomics approach delivers highly sensitive and specific metabolite information on various biospecimens. Such an approach may be adopted to monitor biological changes in over 30 relevant metabolic pathways in response to viral infection and also viral therapeutics.
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15
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Lau CHE, Taylor-Bateman V, Vorkas PA, Graça G, Vu THT, Hou L, Chekmeneva E, Ebbels TMD, Chan Q, Van Horn L, Holmes E. Metabolic Signatures of Gestational Weight Gain and Postpartum Weight Loss in a Lifestyle Intervention Study of Overweight and Obese Women. Metabolites 2020; 10:metabo10120498. [PMID: 33291639 PMCID: PMC7761920 DOI: 10.3390/metabo10120498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Overweight and obesity amongst women of reproductive age are increasingly common in developed economies and are shown to adversely affect birth outcomes and both childhood and adulthood health risks in the offspring. Metabolic profiling in conditions of overweight and obesity in pregnancy could potentially be applied to elucidate the molecular basis of the adverse effects of gestational weight gain (GWG) and postpartum weight loss (WL) on future risks for cardiovascular disease (CVD) and other chronic diseases. Methods: Biofluid samples were collected from 114 ethnically diverse pregnant women with body mass index (BMI) between 25 and 40 kg/m2 from Chicago (US), as part of a randomized lifestyle intervention trial (Maternal Offspring Metabolics: Family Intervention Trial; NCT01631747). At 15 weeks, 35 weeks of gestation, and at 1 year postpartum, the blood plasma lipidome and metabolic profile of urine samples were analyzed by liquid chromatography mass spectrometry (LC-MS) and 1H nuclear magnetic resonance spectroscopy (1H NMR) respectively. Results: Urinary 4-deoxyerythronic acid and 4-deoxythreonic acid were found to be positively correlated to BMI. Seventeen plasma lipids were found to be associated with GWG and 16 lipids were found to be associated with WL, which included phosphatidylinositols (PI), phosphatidylcholines (PC), lysophospholipids (lyso-), sphingomyelins (SM) and ether phosphatidylcholine (PC-O). Three phospholipids found to be positively associated with GWG all contained palmitate side-chains, and amongst the 14 lipids that were negatively associated with GWG, seven were PC-O. Six of eight lipids found to be negatively associated with WL contained an 18:2 fatty acid side-chain. Conclusions: Maternal obesity was associated with characteristic urine and plasma metabolic phenotypes, and phospholipid profile was found to be associated with both GWG and postpartum WL in metabolically healthy pregnant women with overweight/obesity. Postpartum WL may be linked to the reduction in the intake of linoleic acid/conjugated linoleic acid food sources in our study population.
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Affiliation(s)
- Chung-Ho E. Lau
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK;
- Correspondence: (C.-H.E.L.); (E.H.)
| | - Victoria Taylor-Bateman
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Panagiotis A. Vorkas
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece
| | - Gonçalo Graça
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK; (G.G.); (T.M.D.E.)
| | - Thanh-Huyen T. Vu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (T.-H.T.V.); (L.H.); (L.V.H.)
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (T.-H.T.V.); (L.H.); (L.V.H.)
| | - Elena Chekmeneva
- National Phenome Centre and Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, UK;
| | - Timothy M. D. Ebbels
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK; (G.G.); (T.M.D.E.)
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK;
- MRC Centre for Environment and Health, Imperial College London, London W2 1PG, UK
| | - Linda Van Horn
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (T.-H.T.V.); (L.H.); (L.V.H.)
| | - Elaine Holmes
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK;
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (C.-H.E.L.); (E.H.)
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16
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Raja G, Jung Y, Jung SH, Kim TJ. 1H-NMR-based metabolomics for cancer targeting and metabolic engineering –A review. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Liu Z, de Vries B, Gerritsen J, Smidt H, Zoetendal EG. Microbiome-based stratification to guide dietary interventions to improve human health. Nutr Res 2020; 82:1-10. [DOI: 10.1016/j.nutres.2020.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
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18
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Nazifova-Tasinova N, Radeva M, Galunska B, Grupcheva C. Metabolomic analysis in ophthalmology. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2020; 164:236-246. [PMID: 32690974 DOI: 10.5507/bp.2020.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
Modern science takes into account phenotype complexity and establishes approaches to track changes on every possible level. Many "omics" studies have been developed over the last decade. Metabolomic analysis enables dynamic measurement of the metabolic response of a living system to a variety of stimuli or genetic modifications. Important targets of metabolomics is biomarker development and translation to the clinic for personalized diagnosis and a greater understanding of disease pathogenesis. The current review highlights the major aspects of metabolomic analysis and its applications for the identification of relevant predictive, diagnostic and prognostic biomarkers for some ocular diseases including dry eye, keratoconus, retinal diseases, macular degeneration, and glaucoma. To date, possible biomarker candidates for dry eye disease are lipid metabolites and androgens, for keratoconus cytokeratins, urea, citrate cycle, and oxidative stress metabolites. Palmitoylcarnitine, sphingolipids, vitamin D related metabolites, and steroid precursors may be used for distinguishing glaucoma patients from healthy controls. Dysregulation of amino acid and carnitine metabolism is critical in the development and progression of diabetic retinopathy. Further work is needed to discover and validate metabolic biomarkers as a powerful tool for understanding the molecular mechanisms of ocular diseases, to provide knowledge on their etiology and pathophysiology and opportunities for personalized clinical intervention at an early stage.
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Affiliation(s)
- Neshe Nazifova-Tasinova
- Department of Biochemistry, Molecular medicine and Nutrigenomics, Faculty of Pharmacy, Medical University of Varna, 84 Tzar Osvoboditel street, 9000 Varna, Bulgaria
| | - Mladena Radeva
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine, Medical University of Varna, 15 Doyran street, 9000 Varna, Bulgaria
| | - Bistra Galunska
- Department of Biochemistry, Molecular medicine and Nutrigenomics, Faculty of Pharmacy, Medical University of Varna, 84 Tzar Osvoboditel street, 9000 Varna, Bulgaria
| | - Christina Grupcheva
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine, Medical University of Varna, 15 Doyran street, 9000 Varna, Bulgaria
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19
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Chanda P, Costa E, Hu J, Sukumar S, Van Hemert J, Walia R. Information Theory in Computational Biology: Where We Stand Today. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E627. [PMID: 33286399 PMCID: PMC7517167 DOI: 10.3390/e22060627] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 12/30/2022]
Abstract
"A Mathematical Theory of Communication" was published in 1948 by Claude Shannon to address the problems in the field of data compression and communication over (noisy) communication channels. Since then, the concepts and ideas developed in Shannon's work have formed the basis of information theory, a cornerstone of statistical learning and inference, and has been playing a key role in disciplines such as physics and thermodynamics, probability and statistics, computational sciences and biological sciences. In this article we review the basic information theory based concepts and describe their key applications in multiple major areas of research in computational biology-gene expression and transcriptomics, alignment-free sequence comparison, sequencing and error correction, genome-wide disease-gene association mapping, metabolic networks and metabolomics, and protein sequence, structure and interaction analysis.
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Affiliation(s)
- Pritam Chanda
- Corteva Agriscience™, Indianapolis, IN 46268, USA
- Computer and Information Science, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Eduardo Costa
- Corteva Agriscience™, Mogi Mirim, Sao Paulo 13801-540, Brazil
| | - Jie Hu
- Corteva Agriscience™, Indianapolis, IN 46268, USA
| | | | | | - Rasna Walia
- Corteva Agriscience™, Johnston, IA 50131, USA
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20
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Everett JR. Pharmacometabonomics: The Prediction of Drug Effects Using Metabolic Profiling. Handb Exp Pharmacol 2019; 260:263-299. [PMID: 31823071 DOI: 10.1007/164_2019_316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabonomics, also known as metabolomics, is concerned with the study of metabolite profiles in humans, animals, plants and other systems in order to assess their health or other status and their responses to experimental interventions. Metabonomics is thus widely used in disease diagnosis and in understanding responses to therapies such as drug administration. Pharmacometabonomics, also known as pharmacometabolomics, is a related methodology but with a prognostic as opposed to diagnostic thrust. Pharmacometabonomics aims to predict drug effects including efficacy, safety, metabolism and pharmacokinetics, prior to drug administration, via an analysis of pre-dose metabolite profiles. This article will review the development of pharmacometabonomics as a new field of science that has much promise in helping to deliver more effective personalised medicine, a major goal of twenty-first century healthcare.
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Affiliation(s)
- Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Kent, UK.
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