Functional metabolomics: from biomarker discovery to metabolome reprogramming

Peng, Bo; Li, Hui; Peng, Xuan-Xian

doi:10.1007/s13238-015-0185-x

Title: Functional metabolomics: from biomarker discovery to metabolome reprogramming

Abstract

Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.

Authors:

Peng, Bo ^[1]; Li, Hui ^[2]; Peng, Xuan-Xian ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry
Sun Yat-Sen Univ., Guangzhou (China). School of Life Sciences. MOE Key Lab Aquat Food Safety. School of Life Sciences. State Key Lab. of Biocontrol. Center for Proteomics and Metabolomics

Publication Date:: Thu Jul 02 00:00:00 EDT 2015

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1623629

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Protein & Cell

Additional Journal Information:: Journal Volume: 6; Journal Issue: 9; Journal ID: ISSN 1674-800X

Publisher:: Springer

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Cell Biology; metabolomics; discovery metabolomics; reprogramming metabolomics; metabolic strategy; metabolic regulation

Citation Formats


                    Peng, Bo, Li, Hui, and Peng, Xuan-Xian. Functional metabolomics: from biomarker discovery to metabolome reprogramming.  United States: N. p., 2015. 
Web.  doi:10.1007/s13238-015-0185-x.

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                    Peng, Bo, Li, Hui, & Peng, Xuan-Xian. Functional metabolomics: from biomarker discovery to metabolome reprogramming.  United States.  https://doi.org/10.1007/s13238-015-0185-x

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                    Peng, Bo, Li, Hui, and Peng, Xuan-Xian. Thu .  
"Functional metabolomics: from biomarker discovery to metabolome reprogramming".  United States.  https://doi.org/10.1007/s13238-015-0185-x.  https://www.osti.gov/servlets/purl/1623629.

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@article{osti_1623629,

  title        = {Functional metabolomics: from biomarker discovery to metabolome reprogramming},

  author       = {Peng, Bo and Li, Hui and Peng, Xuan-Xian},

  abstractNote = {Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.},

  doi          = {10.1007/s13238-015-0185-x},

  journal      = {Protein & Cell},

  number       = 9,

  volume       = 6,

  place        = {United States},

  year         = {Thu Jul 02 00:00:00 EDT 2015},

  month        = {Thu Jul 02 00:00:00 EDT 2015}

}

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Similar Records

Title: Functional metabolomics: from biomarker discovery to metabolome reprogramming

Abstract

Citation Formats

Redox Metabolites Signal Polymicrobial Biofilm Development via the NapA Oxidative Stress Cascade in Aspergillus journal, January 2015

Women with preterm birth have a distinct cervicovaginal metabolome journal, June 2015

Ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice journal, March 2015

NMR-based metabolomics: From sample preparation to applications in nutrition research journal, November 2014

Targeting of the Hydrophobic Metabolome by Pathogens: Role of the Lipidome in Host-Pathogen Interactions journal, April 2015

Genome-wide association studies with metabolomics journal, January 2012

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes journal, January 2012

Current approaches and challenges for the metabolite profiling of complex natural extracts journal, February 2015

Metabolomics as a tool in nutritional research journal, January 2015

Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva journal, December 2014

Metabolomic Differentiation of Nutritional Stress in an Aquatic Invertebrate journal, January 2015

Editorial on “Current approaches and challenges for the metabolite profiling of complex natural extracts” by Jean-Luc Wolfender, Guillaume Marti, Aurélien Thomas and Samuel Bertrand journal, February 2015

Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review journal, January 2015

Metabolic Phenotyping and Systems Biology Approaches to Understanding Metabolic Syndrome and Fatty Liver Disease journal, January 2014

Metabolomics as a Tool for Drug Discovery and Personalised Medicine. A Review journal, January 2015

Mass-spectrometry-based microbial metabolomics: recent developments and applications journal, September 2014

Newborn Meconium and Urinary Metabolome Response to Maternal Gestational Diabetes Mellitus: A Preliminary Case–Control Study journal, March 2015

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome journal, February 2013

Untargeted Metabolomics: an Emerging Approach to Determine the Composition of Herbal Products journal, January 2013

Proteomics and its applications to aquaculture in China: Infection, immunity, and interaction of aquaculture hosts with pathogens journal, January 2013

Boosting Bacterial Metabolism to Combat Antibiotic Resistance journal, February 2015

N-acetylglucosamine enhances survival ability of tilapias infected by Streptococcus iniae journal, October 2014

SHMT2 drives glioma cell survival in ischaemia but imposes a dependence on glycine clearance journal, April 2015

Integrated metabolomics for abiotic stress responses in plants journal, April 2015

Liver functional metabolomics discloses an action of l-leucine against Streptococcus iniae infection in tilapias journal, August 2015

LC-based targeted metabolomics analysis of nucleotides and identification of biomarkers associated with chemotherapeutic drugs in cultured cell models journal, July 2014

Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses journal, March 2015

Exogenous Alanine and/or Glucose plus Kanamycin Kills Antibiotic-Resistant Bacteria journal, February 2015

Metabonomic analysis of serum of workers occupationally exposed to arsenic, cadmium and lead for biomarker research: A preliminary study journal, July 2014

Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products journal, January 2014

Genome-Wide Association Studies with Metabolomics book, January 2012

Linking diet, physical activity, cardiorespiratory fitness and obesity to serum metabolite networks: findings from a population-based study journal, March 2014

Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva journal, December 2014

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes journal, January 2012

High-throughput discovery metabolomics journal, February 2015

Metabolic response of maize plants to multi-factorial abiotic stresses journal, January 2015

Human metabolic individuality in biomedical and pharmaceutical research journal, August 2011

Studies of metabolite–protein interactions: A review journal, September 2014

Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells journal, December 2014

CE-MS for metabolomics: Developments and applications in the period 2012-2014: CE and CEC journal, November 2014

Redox Metabolites Signal Polymicrobial Biofilm Development via the NapA Oxidative Stress Cascade in Aspergillus journal, January 2015

l-proline increases survival of tilapias infected by Streptococcus agalactiae in higher water temperature journal, May 2015

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome journal, February 2013

Impact of Antibiotics with Various Target Sites on the Metabolome of Staphylococcus aureus journal, September 2014

Succinate is an inflammatory signal that induces IL-1β through HIF-1α journal, March 2013

Interferon-α2b against Microbes through Promoting Biosynthesis of Unsaturated Fatty Acids journal, July 2014

Potential of metabolomics in preclinical and clinical drug development journal, December 2014

Metagenomic and Metabolomic Analysis of the Toxic Effects of Trichloroacetamide-Induced Gut Microbiome and Urine Metabolome Perturbations in Mice journal, February 2015

Time-dependent metabolomic profiling of Ketamine drug action reveals hippocampal pathway alterations and biomarker candidates journal, November 2014

Integrated comparative metabolite profiling via MS and NMR techniques for Senna drug quality control analysis journal, January 2015

NMR-based metabolomics: From sample preparation to applications in nutrition research journal, November 2014

Human Metabolic Individuality in Biomedical and Pharmaceutical Research journal, December 2011

Metabolomics as a Tool for Drug Discovery and Personalised Medicine. A Review journal, January 2015

Metabolomic analysis reveals rewiring of S ynechocystis sp. PCC 6803 primary metabolism by ntcA overexpression: Rewiring of Synechocystis metabolism by NtcA journal, August 2014

Women with preterm birth have a distinct cervicovaginal metabolome journal, June 2015

Urinary Metabolomics Revealed Arsenic Internal Dose-Related Metabolic Alterations: A Proof-of-Concept Study in a Chinese Male Cohort journal, October 2014

Metabonomic analysis of serum of workers occupationally exposed to arsenic, cadmium and lead for biomarker research: A preliminary study journal, July 2014

Exogenous Alanine and/or Glucose plus Kanamycin Kills Antibiotic-Resistant Bacteria journal, February 2015

Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review journal, January 2015

Fructose Restores Susceptibility of Multidrug-Resistant Edwardsiella tarda to Kanamycin journal, February 2015

Emerging field of metabolomics: Big promise for cancer biomarker identification and drug discovery journal, March 2015

Glutamate enrichment as new diagnostic opportunity in breast cancer: Glutamate and Glutamine in Breast Cancer journal, September 2014

Metabolic Phenotyping in Health and Disease journal, September 2008

mSphere of Influence: Host Metabolism Is an Integral Part of the Immune Response to Infectious Diseases journal, August 2021

Current approaches and challenges for the metabolite profiling of complex natural extracts journal, February 2015

Downregulation of Na(+)–NQR complex is essential for Vibrio alginolyticus in resistance to balofloxacin journal, May 2012

Proteomics and its applications to aquaculture in China: Infection, immunity, and interaction of aquaculture hosts with pathogens journal, January 2013

Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress: MASS SPECTROMETRY-BASED PLANT METABOLOMICS journal, January 2015

Exogenous glycine and serine promote growth and antifungal activity of Penicillium citrinum W1 from the south-west Indian Ocean journal, March 2015

N-acetylglucosamine enhances survival ability of tilapias infected by Streptococcus iniae journal, October 2014

Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells journal, December 2014

Decreased expression of LamB and Odp1 complex is crucial for antibiotic resistance in Escherichia coli journal, February 2014

Human metabolic individuality in biomedical and pharmaceutical research journal, August 2011

SHMT2 drives glioma cell survival in ischaemia but imposes a dependence on glycine clearance journal, April 2015

Integrated metabolomics for abiotic stress responses in plants journal, April 2015

l-proline increases survival of tilapias infected by Streptococcus agalactiae in higher water temperature journal, May 2015

Boosting Bacterial Metabolism to Combat Antibiotic Resistance journal, February 2015

Redox Metabolites Signal Polymicrobial Biofilm Development via the NapA Oxidative Stress Cascade in Aspergillus
journal, January 2015

Women with preterm birth have a distinct cervicovaginal metabolome
journal, June 2015

Ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice
journal, March 2015

NMR-based metabolomics: From sample preparation to applications in nutrition research
journal, November 2014

Targeting of the Hydrophobic Metabolome by Pathogens: Role of the Lipidome in Host-Pathogen Interactions
journal, April 2015

Genome-wide association studies with metabolomics
journal, January 2012

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes
journal, January 2012

Current approaches and challenges for the metabolite profiling of complex natural extracts
journal, February 2015

Metabolomics as a tool in nutritional research
journal, January 2015

Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva
journal, December 2014

Metabolomic Differentiation of Nutritional Stress in an Aquatic Invertebrate
journal, January 2015

Editorial on “Current approaches and challenges for the metabolite profiling of complex natural extracts” by Jean-Luc Wolfender, Guillaume Marti, Aurélien Thomas and Samuel Bertrand
journal, February 2015

Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review
journal, January 2015

Metabolic Phenotyping and Systems Biology Approaches to Understanding Metabolic Syndrome and Fatty Liver Disease
journal, January 2014

Metabolomics as a Tool for Drug Discovery and Personalised Medicine. A Review
journal, January 2015

Mass-spectrometry-based microbial metabolomics: recent developments and applications
journal, September 2014

Newborn Meconium and Urinary Metabolome Response to Maternal Gestational Diabetes Mellitus: A Preliminary Case–Control Study
journal, March 2015

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome
journal, February 2013

Untargeted Metabolomics: an Emerging Approach to Determine the Composition of Herbal Products
journal, January 2013

Proteomics and its applications to aquaculture in China: Infection, immunity, and interaction of aquaculture hosts with pathogens
journal, January 2013

Boosting Bacterial Metabolism to Combat Antibiotic Resistance
journal, February 2015

N-acetylglucosamine enhances survival ability of tilapias infected by Streptococcus iniae
journal, October 2014

SHMT2 drives glioma cell survival in ischaemia but imposes a dependence on glycine clearance
journal, April 2015

Integrated metabolomics for abiotic stress responses in plants
journal, April 2015

Liver functional metabolomics discloses an action of l-leucine against Streptococcus iniae infection in tilapias
journal, August 2015

LC-based targeted metabolomics analysis of nucleotides and identification of biomarkers associated with chemotherapeutic drugs in cultured cell models
journal, July 2014

Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses
journal, March 2015

Exogenous Alanine and/or Glucose plus Kanamycin Kills Antibiotic-Resistant Bacteria
journal, February 2015

Metabonomic analysis of serum of workers occupationally exposed to arsenic, cadmium and lead for biomarker research: A preliminary study
journal, July 2014

Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products
journal, January 2014

Genome-Wide Association Studies with Metabolomics
book, January 2012

Linking diet, physical activity, cardiorespiratory fitness and obesity to serum metabolite networks: findings from a population-based study
journal, March 2014

Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva
journal, December 2014

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes
journal, January 2012

High-throughput discovery metabolomics
journal, February 2015

Metabolic response of maize plants to multi-factorial abiotic stresses
journal, January 2015

Human metabolic individuality in biomedical and pharmaceutical research
journal, August 2011

Studies of metabolite–protein interactions: A review
journal, September 2014

Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells
journal, December 2014

CE-MS for metabolomics: Developments and applications in the period 2012-2014: CE and CEC
journal, November 2014

Redox Metabolites Signal Polymicrobial Biofilm Development via the NapA Oxidative Stress Cascade in Aspergillus
journal, January 2015

l-proline increases survival of tilapias infected by Streptococcus agalactiae in higher water temperature
journal, May 2015

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome
journal, February 2013

Impact of Antibiotics with Various Target Sites on the Metabolome of Staphylococcus aureus
journal, September 2014

Succinate is an inflammatory signal that induces IL-1β through HIF-1α
journal, March 2013

Interferon-α2b against Microbes through Promoting Biosynthesis of Unsaturated Fatty Acids
journal, July 2014

Potential of metabolomics in preclinical and clinical drug development
journal, December 2014

Metagenomic and Metabolomic Analysis of the Toxic Effects of Trichloroacetamide-Induced Gut Microbiome and Urine Metabolome Perturbations in Mice
journal, February 2015

Time-dependent metabolomic profiling of Ketamine drug action reveals hippocampal pathway alterations and biomarker candidates
journal, November 2014

Integrated comparative metabolite profiling via MS and NMR techniques for Senna drug quality control analysis
journal, January 2015

NMR-based metabolomics: From sample preparation to applications in nutrition research
journal, November 2014

Human Metabolic Individuality in Biomedical and Pharmaceutical Research
journal, December 2011

Metabolomics as a Tool for Drug Discovery and Personalised Medicine. A Review
journal, January 2015

Metabolomic analysis reveals rewiring of S ynechocystis sp. PCC 6803 primary metabolism by ntcA overexpression: Rewiring of Synechocystis metabolism by NtcA
journal, August 2014

Women with preterm birth have a distinct cervicovaginal metabolome
journal, June 2015

Urinary Metabolomics Revealed Arsenic Internal Dose-Related Metabolic Alterations: A Proof-of-Concept Study in a Chinese Male Cohort
journal, October 2014

Metabonomic analysis of serum of workers occupationally exposed to arsenic, cadmium and lead for biomarker research: A preliminary study
journal, July 2014

Exogenous Alanine and/or Glucose plus Kanamycin Kills Antibiotic-Resistant Bacteria
journal, February 2015

Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review
journal, January 2015

Fructose Restores Susceptibility of Multidrug-Resistant Edwardsiella tarda to Kanamycin
journal, February 2015

Emerging field of metabolomics: Big promise for cancer biomarker identification and drug discovery
journal, March 2015

Glutamate enrichment as new diagnostic opportunity in breast cancer: Glutamate and Glutamine in Breast Cancer
journal, September 2014

Metabolic Phenotyping in Health and Disease
journal, September 2008

mSphere of Influence: Host Metabolism Is an Integral Part of the Immune Response to Infectious Diseases
journal, August 2021

Current approaches and challenges for the metabolite profiling of complex natural extracts
journal, February 2015

Downregulation of Na(+)–NQR complex is essential for Vibrio alginolyticus in resistance to balofloxacin
journal, May 2012

Proteomics and its applications to aquaculture in China: Infection, immunity, and interaction of aquaculture hosts with pathogens
journal, January 2013

Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress: MASS SPECTROMETRY-BASED PLANT METABOLOMICS
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